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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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"01:10 1.1Gb 100.0% Build index\r",
"\r\n"
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"text": [
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"text": [
"01:11 1.1Gb 2.0% Rows\r"
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"01:12 1.1Gb 11.9% Rows\r"
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"01:13 1.1Gb 21.0% Rows\r"
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"01:14 1.1Gb 26.3% Rows\r"
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"01:15 1.1Gb 42.0% Rows\r"
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"01:16 1.1Gb 61.2% Rows\r"
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"text": [
"01:17 1.1Gb 66.1% Rows\r"
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},
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"text": [
"01:18 1.1Gb 69.7% Rows\r"
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"01:19 1.1Gb 79.5% Rows\r"
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"01:20 1.1Gb 94.7% Rows\r"
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"text": [
"01:20 1.1Gb 100.0% Rows\r",
"\r\n",
"01:20 1.1Gb Buffers \r\n"
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},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"01:20 1.1Gb 0.0% Seqs\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"01:21 1.1Gb 8.0% Seqs\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"01:22 1.1Gb 48.1% Seqs\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"01:23 1.1Gb 94.9% Seqs\r",
"01:23 1.1Gb 100.0% Seqs\r",
"\r\n"
]
},
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"output_type": "stream",
"stream": "stdout",
"text": [
"01:23 1.1Gb 100.0% completed, split 1 (542.0k seqs)\r\n",
"01:23 1.1Gb Total 1 splits, 542.0k seqs\r\n"
]
}
],
"prompt_number": 12
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{
"cell_type": "code",
"collapsed": false,
"input": [
"!usearch -udbinfo /Volumes/Bay3/usearch/uniprot_sprot.udb\n"
],
"language": "python",
"metadata": {},
"outputs": [
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"output_type": "stream",
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"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
" Splits 1\r\n",
" Seqs 541954 (542.0k)\r\n",
" Hashed 0\r\n",
" SeqIx bits 21\r\n",
" SeqPos bits 11\r\n",
" Alpha A,KR,DENQ,C,G,H,ILMV,FWY,P,ST (10)\r\n",
" Pattern \"10111011\" (6,8)\r\n",
" Word width 0\r\n",
" Slots 0\r\n",
" Dict size 1000000 (1.0M)\r\n",
" DBStep 1\r\n",
" StepPrefix \"\"\r\n",
" DBAccel 100%\r\n",
" Split 1, 964.6M bytes\r\n"
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"input": [
"%%time\n",
"!usearch -ublast /Volumes/web/scaphapoda/Grace/Transcriptomes/mer_tst/query.fa \\\n",
"-db /Volumes/Bay3/usearch/uniprot_sprot.udb \\\n",
"-evalue 1e-5 \\\n",
"-accel 0.9 \\\n",
"-top_hits_only \\\n",
"-maxhits 1 \\\n",
"-blast6out /Volumes/Bay3/usearch/results.b6\n"
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"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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"output_type": "stream",
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"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
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},
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 95.5% Searching, 7.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 100.0% Searching, 6.3% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"CPU times: user 26.2 ms, sys: 14.6 ms, total: 40.8 ms\n",
"Wall time: 3.47 s\n"
]
}
],
"prompt_number": 63
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/Bay3/usearch/results.b6\n"
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"language": "python",
"metadata": {},
"outputs": [
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"output_type": "stream",
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"text": [
"Mmercenaria_Contig_2\tsp|Q6DRI1|EI3EA_DANRE\t72.9\t70\t19\t0\t2\t211\t113\t182\t2.5e-24\t112.1\r\n",
"Mmercenaria_Contig_9\tsp|A8WGF4|IF122_XENTR\t67.2\t67\t22\t0\t1\t201\t894\t960\t6.4e-20\t97.4\r\n",
"Mmercenaria_Contig_11\tsp|Q3SZI6|RPN2_BOVIN\t32.4\t71\t48\t0\t2\t214\t223\t293\t4.2e-06\t51.6\r\n",
"Mmercenaria_Contig_21\tsp|Q95JL5|WDR16_MACFA\t65.0\t80\t28\t0\t5\t244\t467\t546\t1.6e-25\t116.3\r\n",
"Mmercenaria_Contig_20\tsp|Q7Z7J7|LHPL4_HUMAN\t43.3\t67\t38\t0\t18\t218\t4\t70\t1.1e-11\t70.1\r\n",
"Mmercenaria_Contig_23\tsp|Q90512|ODO2_TAKRU\t62.3\t77\t29\t0\t2\t232\t27\t103\t5.6e-22\t104.4\r\n",
"Mmercenaria_Contig_24\tsp|Q29RL1|CF165_BOVIN\t72.4\t76\t21\t0\t1\t228\t64\t139\t1.8e-25\t115.9\r\n",
"Mmercenaria_Contig_32\tsp|Q54YM7|TM2D2_DICDI\t57.4\t54\t23\t0\t6\t167\t58\t111\t4e-11\t68.6\r\n",
"Mmercenaria_Contig_37\tsp|P50579|MAP2_HUMAN\t85.9\t92\t13\t0\t2\t277\t338\t429\t3.8e-41\t168.3\r\n",
"Mmercenaria_Contig_36\tsp|O14508|SOCS2_HUMAN\t39.7\t146\t75\t2\t3\t440\t64\t196\t8.3e-22\t104.8\r\n"
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"input": [
"%%time\n",
"!/Volumes/Bay3/Software/ncbi-blast-2.2.29+/bin/blastx \\\n",
"-query /Volumes/web/scaphapoda/Grace/Transcriptomes/mer_tst/query.fa \\\n",
"-db /Volumes/Bay3/Software/ncbi-blast-2.2.28+/db/uniprot_sprot \\\n",
"-evalue 1e-5 \\\n",
"-max_target_seqs 1 \\\n",
"-outfmt 6 \\\n",
"-num_threads 2 \\\n",
"-out /Volumes/Bay3/usearch/ncbi_results.b6"
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"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"CPU times: user 173 ms, sys: 43.1 ms, total: 216 ms\n",
"Wall time: 30.9 s\n"
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}
],
"prompt_number": 66
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"cell_type": "code",
"collapsed": false,
"input": [
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"text": [
"Mmercenaria_Contig_2\tsp|Q6DRI1|EI3EA_DANRE\t75.00\t68\t17\t0\t5\t208\t114\t181\t2e-29\t 112\r\n",
"Mmercenaria_Contig_9\tsp|A8WGF4|IF122_XENTR\t67.16\t67\t22\t0\t1\t201\t894\t960\t6e-24\t99.4\r\n",
"Mmercenaria_Contig_20\tsp|Q7Z7J7|LHPL4_HUMAN\t48.33\t60\t31\t0\t24\t203\t6\t65\t2e-15\t71.6\r\n",
"Mmercenaria_Contig_21\tsp|Q95JL5|WDR16_MACFA\t65.00\t80\t28\t0\t5\t244\t467\t546\t5e-30\t 115\r\n",
"Mmercenaria_Contig_23\tsp|Q90512|ODO2_TAKRU\t62.34\t77\t29\t0\t2\t232\t27\t103\t1e-26\t 103\r\n",
"Mmercenaria_Contig_24\tsp|Q6PE87|CF165_MOUSE\t73.68\t76\t20\t0\t1\t228\t64\t139\t1e-31\t 119\r\n",
"Mmercenaria_Contig_32\tsp|Q9GPR3|TM2D1_DICDI\t56.60\t53\t23\t0\t6\t164\t9\t61\t3e-12\t62.8\r\n",
"Mmercenaria_Contig_36\tsp|O14508|SOCS2_HUMAN\t40.28\t144\t73\t2\t9\t440\t66\t196\t2e-25\t 102\r\n",
"Mmercenaria_Contig_37\tsp|P50579|MAP2_HUMAN\t85.87\t92\t13\t0\t2\t277\t338\t429\t2e-51\t 173\r\n"
]
}
],
"prompt_number": 67
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l /Volumes/Bay3/usearch/ncbi_results.b6"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 9 /Volumes/Bay3/usearch/ncbi_results.b6\r\n"
]
}
],
"prompt_number": 68
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"cgigas file"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cp /Volumes/web/astrangia/cgigas /Volumes/Bay3/usearch/cgigas.fa"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 73
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/Bay3/usearch/cgigas.fa"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
">AJ565444.p.cg.8\r\n",
"GTACGTAATTGCTGTTTTGTTTTAAAACAAATATTTGTTTAAATTATCAA\r\n",
"AATAGGAGAATCGATTAAACCCAGATGCTTTCCGTCGGAGACAGAATCAA\r\n",
"AAACTGTGAATGTAACAGAAGACAAACCAGTTGGGTTCACCGTGTTCACT\r\n",
"TATTCGGGTTTTGATGCTGATGGAGATCGCATTAGATTTGTGTTACTTGA\r\n",
"TAACACGGTGCCGTTCTCGATTCCAACAGCAGGATCCGGGGATGTTGATG\r\n",
"TGGCTTTACCTGCCTTAGACTTTGAGAGGAAAACTCAATATATTTTGGAC\r\n",
"AAAATATACGTCACTAAATTTGGATTGAGTGCACTCCTGTTTGGTAATAA\r\n",
"ATGTGGAACCCTAACCGTCAATGTCCTCCCTGTCAACGAATTTACGCCAG\r\n",
"TTTTTGATCCCTCATATCAAAATTCCTCACTTCCAGAAGGTCTACTACAA\r\n"
]
}
],
"prompt_number": 76
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd /Volumes/web/cnidarian"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/web/cnidarian\n"
]
}
],
"prompt_number": 82
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"mkdir cg_split"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 83
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd cg_split"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/web/cnidarian/cg_split\n"
]
}
],
"prompt_number": 84
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!perl /Volumes/Bay3/Software/fasta-splitter.pl --part-size 1000 --measure count /Volumes/Bay3/usearch/cgigas.fa "
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/Bay3/usearch/cgigas.fa"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
": 82312 sequences, 67875621 bp => dividing into 83 parts of <= 1000 sequences\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"All done, 8 seconds elapsed\r\n"
]
}
],
"prompt_number": 85
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ls"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"cgigas.part-01.fa cgigas.part-22.fa cgigas.part-43.fa cgigas.part-64.fa\r\n",
"cgigas.part-02.fa cgigas.part-23.fa cgigas.part-44.fa cgigas.part-65.fa\r\n",
"cgigas.part-03.fa cgigas.part-24.fa cgigas.part-45.fa cgigas.part-66.fa\r\n",
"cgigas.part-04.fa cgigas.part-25.fa cgigas.part-46.fa cgigas.part-67.fa\r\n",
"cgigas.part-05.fa cgigas.part-26.fa cgigas.part-47.fa cgigas.part-68.fa\r\n",
"cgigas.part-06.fa cgigas.part-27.fa cgigas.part-48.fa cgigas.part-69.fa\r\n",
"cgigas.part-07.fa cgigas.part-28.fa cgigas.part-49.fa cgigas.part-70.fa\r\n",
"cgigas.part-08.fa cgigas.part-29.fa cgigas.part-50.fa cgigas.part-71.fa\r\n",
"cgigas.part-09.fa cgigas.part-30.fa cgigas.part-51.fa cgigas.part-72.fa\r\n",
"cgigas.part-10.fa cgigas.part-31.fa cgigas.part-52.fa cgigas.part-73.fa\r\n",
"cgigas.part-11.fa cgigas.part-32.fa cgigas.part-53.fa cgigas.part-74.fa\r\n",
"cgigas.part-12.fa cgigas.part-33.fa cgigas.part-54.fa cgigas.part-75.fa\r\n",
"cgigas.part-13.fa cgigas.part-34.fa cgigas.part-55.fa cgigas.part-76.fa\r\n",
"cgigas.part-14.fa cgigas.part-35.fa cgigas.part-56.fa cgigas.part-77.fa\r\n",
"cgigas.part-15.fa cgigas.part-36.fa cgigas.part-57.fa cgigas.part-78.fa\r\n",
"cgigas.part-16.fa cgigas.part-37.fa cgigas.part-58.fa cgigas.part-79.fa\r\n",
"cgigas.part-17.fa cgigas.part-38.fa cgigas.part-59.fa cgigas.part-80.fa\r\n",
"cgigas.part-18.fa cgigas.part-39.fa cgigas.part-60.fa cgigas.part-81.fa\r\n",
"cgigas.part-19.fa cgigas.part-40.fa cgigas.part-61.fa cgigas.part-82.fa\r\n",
"cgigas.part-20.fa cgigas.part-41.fa cgigas.part-62.fa cgigas.part-83.fa\r\n",
"cgigas.part-21.fa cgigas.part-42.fa cgigas.part-63.fa\r\n"
]
}
],
"prompt_number": 174
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd /Volumes/web/cnidarian/cg_split"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/web/cnidarian/cg_split\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head cgigas.part-01.fa"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
">AM859803.p.cg.8\r\n",
"ACGCTCCTCGGTTTTTTGATACGGGGAGCGGATGGAATTAATTTGTGATGGACTGGTGGC\r\n",
"ACATTCAGGGTGAACCGATGACTTTCATTGCTTAGCAGCACGGAAACCGCGGATAAGCAT\r\n",
"CGGCCCTATACGACTCATGGCGTGGGGAAGGGTTTGTATTTTAGCTTGTTTTCATATCAA\r\n",
"TTGGACAAAATTTTGATTAATGCGCACAACCCTTCATTTTCGTCTTCTCCAACCTTTGGT\r\n",
"GTTTGGTGTGTATATACAGGTATTGTGTTACTTACCTGTACATGAAGCAGGATGACTTAA\r\n",
"TTTTATACCTGACATATCACTTTTGATGTCAGACAGAATTTAAACAGTACAGCGCTGGTA\r\n",
"CCTGATACTTTCGTTTGCATGTTTTCAATGTATGCACTATCACGGAATTAATTTCAATCT\r\n",
"CTAGGCATTTTCAAATTGCTCTATATAAAGATTCTTACTGGCTCCACTTTTTACATCGGT\r\n",
"TCTCAATATTTTTTTAACACTTTTACATTTTGATTGGTGCTTCAACCTTTCAGGTTGATG\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pwd"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 3,
"text": [
"u'/Volumes/web/cnidarian/cg_split'"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from __future__ import print_function\n",
"import glob\n",
"import os\n",
"os.chdir(\"/Volumes/web/cnidarian/cg_split\")\n",
"for file in glob.glob(\"*\"):\n",
" !usearch -ublast $file -db /Volumes/Bay3/usearch/uniprot_sprot.udb \\\n",
" -evalue 1e-5 \\\n",
" -accel 0.2 \\\n",
" -top_hits_only \\\n",
" -maxhits 1 \\\n",
" -blast6out /Volumes/web/cnidarian/$file._ublast_sprot.b6\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Invalid command line\r\n",
"Expected -option_name or --option_name, got '/Volumes/Bay3/usearch/uniprot_sprot.udb'\r\n"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for i in \"*\":\n",
" !/Volumes/Bay3/Software/ncbi-blast-2.2.29+/bin/blastx \\\n",
"-query {i} \\\n",
"-db /Volumes/Bay3/Software/ncbi-blast-2.2.28+/db/uniprot_sprot \\\n",
"-evalue 1e-5 \\\n",
"-max_target_seqs 1 \\\n",
"-outfmt 6 \\\n",
"-num_threads 2 \\\n",
"-out /Volumes/Bay3/usearch/ncbi_{i}results.b6\n",
"!say done"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"USAGE\r\n",
" blastx [-h] [-help] [-import_search_strategy filename]\r\n",
" [-export_search_strategy filename] [-db database_name]\r\n",
" [-dbsize num_letters] [-gilist filename] [-seqidlist filename]\r\n",
" [-negative_gilist filename] [-entrez_query entrez_query]\r\n",
" [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]\r\n",
" [-subject subject_input_file] [-subject_loc range] [-query input_file]\r\n",
" [-out output_file] [-evalue evalue] [-word_size int_value]\r\n",
" [-gapopen open_penalty] [-gapextend extend_penalty]\r\n",
" [-xdrop_ungap float_value] [-xdrop_gap float_value]\r\n",
" [-xdrop_gap_final float_value] [-searchsp int_value] [-max_hsps int_value]\r\n",
" [-sum_statistics] [-max_intron_length length] [-seg SEG_options]\r\n",
" [-soft_masking soft_masking] [-matrix matrix_name]\r\n",
" [-threshold float_value] [-culling_limit int_value]\r\n",
" [-best_hit_overhang float_value] [-best_hit_score_edge float_value]\r\n",
" [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]\r\n",
" [-strand strand] [-parse_deflines] [-query_gencode int_value]\r\n",
" [-outfmt format] [-show_gis] [-num_descriptions int_value]\r\n",
" [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]\r\n",
" [-num_threads int_value] [-remote] [-comp_based_stats compo]\r\n",
" [-use_sw_tback] [-version]\r\n",
"\r\n",
"DESCRIPTION\r\n",
" Translated Query-Protein Subject BLAST 2.2.29+\r\n",
"\r\n",
"Use '-help' to print detailed descriptions of command line arguments\r\n",
"========================================================================\r\n",
"\r\n",
"Error: Too many positional arguments (1), the offending value: cgigas.part-02.fa\r\n"
]
}
],
"prompt_number": 200
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from __future__ import print_function\n",
"import glob\n",
"import os\n",
"os.chdir(\"/Volumes/web/cnidarian/cg_split\")\n",
"for file in glob.glob(\"*\"):\n",
" /Volumes/Bay3/Software/ncbi-blast-2.2.29+/bin/blastx -query $file \\\n",
" -db /Volumes/caviar/Dropbox/Steven/eimd/data/blast_db/Biosystem_751435 \\\n",
" -out /Volumes/web/cnidarian/$file.blastout"
],
"language": "python",
"metadata": {},
"outputs": [
{
"ename": "SyntaxError",
"evalue": "invalid syntax (, line 6)",
"output_type": "pyerr",
"traceback": [
"\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m6\u001b[0m\n\u001b[0;31m Volumes(/Bay3/Software/ncbi-blast-2.2.29+/bin/blastx, -query, $file, -db, /Volumes/caviar/Dropbox/Steven/eimd/data/blast_db/Biosystem_751435, -out, /Volumes/web/cnidarian/$file.blastout)\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
]
}
],
"prompt_number": 12
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for i in (\"cgigas.part-21.fa\",\"cgigas.part-42.fa\"):\n",
" !echo {i} "
],
"language": "python",
"metadata": {},
"outputs": [
{
"ename": "SyntaxError",
"evalue": "invalid syntax (, line 1)",
"output_type": "pyerr",
"traceback": [
"\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m for i in (cgigas.part-01.fa,cgigas.part-02.fa):\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
]
}
],
"prompt_number": 36
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for i in \"*\":\n",
" !echo {i} | tr ' ' , | sed 's/fa/fa\"/g' | sed 's/cgig/\"cgig/g' "
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\"cgigas.part-01.fa\",\"cgigas.part-02.fa\",\"cgigas.part-03.fa\",\"cgigas.part-04.fa\",\"cgigas.part-05.fa\",\"cgigas.part-06.fa\",\"cgigas.part-07.fa\",\"cgigas.part-08.fa\",\"cgigas.part-09.fa\",\"cgigas.part-10.fa\",\"cgigas.part-11.fa\",\"cgigas.part-12.fa\",\"cgigas.part-13.fa\",\"cgigas.part-14.fa\",\"cgigas.part-15.fa\",\"cgigas.part-16.fa\",\"cgigas.part-17.fa\",\"cgigas.part-18.fa\",\"cgigas.part-19.fa\",\"cgigas.part-20.fa\",\"cgigas.part-21.fa\",\"cgigas.part-22.fa\",\"cgigas.part-23.fa\",\"cgigas.part-24.fa\",\"cgigas.part-25.fa\",\"cgigas.part-26.fa\",\"cgigas.part-27.fa\",\"cgigas.part-28.fa\",\"cgigas.part-29.fa\",\"cgigas.part-30.fa\",\"cgigas.part-31.fa\",\"cgigas.part-32.fa\",\"cgigas.part-33.fa\",\"cgigas.part-34.fa\",\"cgigas.part-35.fa\",\"cgigas.part-36.fa\",\"cgigas.part-37.fa\",\"cgigas.part-38.fa\",\"cgigas.part-39.fa\",\"cgigas.part-40.fa\",\"cgigas.part-41.fa\",\"cgigas.part-42.fa\",\"cgigas.part-43.fa\",\"cgigas.part-44.fa\",\"cgigas.part-45.fa\",\"cgigas.part-46.fa\",\"cgigas.part-47.fa\",\"cgigas.part-48.fa\",\"cgigas.part-49.fa\",\"cgigas.part-50.fa\",\"cgigas.part-51.fa\",\"cgigas.part-52.fa\",\"cgigas.part-53.fa\",\"cgigas.part-54.fa\",\"cgigas.part-55.fa\",\"cgigas.part-56.fa\",\"cgigas.part-57.fa\",\"cgigas.part-58.fa\",\"cgigas.part-59.fa\",\"cgigas.part-60.fa\",\"cgigas.part-61.fa\",\"cgigas.part-62.fa\",\"cgigas.part-63.fa\",\"cgigas.part-64.fa\",\"cgigas.part-65.fa\",\"cgigas.part-66.fa\",\"cgigas.part-67.fa\",\"cgigas.part-68.fa\",\"cgigas.part-69.fa\",\"cgigas.part-70.fa\",\"cgigas.part-71.fa\",\"cgigas.part-72.fa\",\"cgigas.part-73.fa\",\"cgigas.part-74.fa\",\"cgigas.part-75.fa\",\"cgigas.part-76.fa\",\"cgigas.part-77.fa\",\"cgigas.part-78.fa\",\"cgigas.part-79.fa\",\"cgigas.part-80.fa\",\"cgigas.part-81.fa\",\"cgigas.part-82.fa\",\"cgigas.part-83.fa\",tmp\r\n"
]
}
],
"prompt_number": 43
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%time\n",
"for i in (\"cgigas.part-01.fa\",\"cgigas.part-02.fa\",\"cgigas.part-03.fa\",\"cgigas.part-04.fa\",\"cgigas.part-05.fa\",\"cgigas.part-06.fa\",\"cgigas.part-07.fa\",\"cgigas.part-08.fa\",\"cgigas.part-09.fa\",\"cgigas.part-10.fa\",\"cgigas.part-11.fa\",\"cgigas.part-12.fa\",\"cgigas.part-13.fa\",\"cgigas.part-14.fa\",\"cgigas.part-15.fa\",\"cgigas.part-16.fa\",\"cgigas.part-17.fa\",\"cgigas.part-18.fa\",\"cgigas.part-19.fa\",\"cgigas.part-20.fa\",\"cgigas.part-21.fa\",\"cgigas.part-22.fa\",\"cgigas.part-23.fa\",\"cgigas.part-24.fa\",\"cgigas.part-25.fa\",\"cgigas.part-26.fa\",\"cgigas.part-27.fa\",\"cgigas.part-28.fa\",\"cgigas.part-29.fa\",\"cgigas.part-30.fa\",\"cgigas.part-31.fa\",\"cgigas.part-32.fa\",\"cgigas.part-33.fa\",\"cgigas.part-34.fa\",\"cgigas.part-35.fa\",\"cgigas.part-36.fa\",\"cgigas.part-37.fa\",\"cgigas.part-38.fa\",\"cgigas.part-39.fa\",\"cgigas.part-40.fa\",\"cgigas.part-41.fa\",\"cgigas.part-42.fa\",\"cgigas.part-43.fa\",\"cgigas.part-44.fa\",\"cgigas.part-45.fa\",\"cgigas.part-46.fa\",\"cgigas.part-47.fa\",\"cgigas.part-48.fa\",\"cgigas.part-49.fa\",\"cgigas.part-50.fa\",\"cgigas.part-51.fa\",\"cgigas.part-52.fa\",\"cgigas.part-53.fa\",\"cgigas.part-54.fa\",\"cgigas.part-55.fa\",\"cgigas.part-56.fa\",\"cgigas.part-57.fa\",\"cgigas.part-58.fa\",\"cgigas.part-59.fa\",\"cgigas.part-60.fa\",\"cgigas.part-61.fa\",\"cgigas.part-62.fa\",\"cgigas.part-63.fa\",\"cgigas.part-64.fa\",\"cgigas.part-65.fa\",\"cgigas.part-66.fa\",\"cgigas.part-67.fa\",\"cgigas.part-68.fa\",\"cgigas.part-69.fa\",\"cgigas.part-70.fa\",\"cgigas.part-71.fa\",\"cgigas.part-72.fa\",\"cgigas.part-73.fa\",\"cgigas.part-74.fa\",\"cgigas.part-75.fa\",\"cgigas.part-76.fa\",\"cgigas.part-77.fa\",\"cgigas.part-78.fa\",\"cgigas.part-79.fa\",\"cgigas.part-80.fa\",\"cgigas.part-81.fa\",\"cgigas.part-82.fa\",\"cgigas.part-83.fa\"):\n",
" !usearch -ublast {i} \\\n",
"-db /Volumes/Bay3/usearch/uniprot_sprot.udb \\\n",
"-evalue 1e-5 \\\n",
"-accel 0.8 \\\n",
"-top_hits_only \\\n",
"-maxhits 1 \\\n",
"-blast6out /Volumes/web/cnidarian/cgigas8_{i}_ublast_sprot.b6\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb Database loaded\r\n",
"00:03 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.5% Searching, 1.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.3% Searching, 2.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:06 1.1Gb 11.0% Searching, 2.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 14.9% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 17.8% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 21.8% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 24.6% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 26.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 28.5% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 31.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
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"text": [
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]
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"00:20 1.1Gb 56.1% Searching, 3.0% matched\r"
]
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]
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"text": [
"00:22 1.1Gb 64.2% Searching, 2.9% matched\r"
]
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"00:23 1.1Gb 67.8% Searching, 2.9% matched\r"
]
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"00:24 1.1Gb 71.8% Searching, 2.9% matched\r"
]
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"00:25 1.1Gb 75.5% Searching, 2.8% matched\r"
]
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"00:26 1.1Gb 79.0% Searching, 2.8% matched\r"
]
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"00:27 1.1Gb 82.5% Searching, 2.8% matched\r"
]
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"text": [
"00:28 1.1Gb 85.5% Searching, 2.8% matched\r"
]
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"output_type": "stream",
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"text": [
"00:29 1.1Gb 89.5% Searching, 2.7% matched\r"
]
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"output_type": "stream",
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"text": [
"00:30 1.1Gb 93.0% Searching, 2.7% matched\r"
]
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"text": [
"00:31 1.1Gb 96.0% Searching, 2.7% matched\r"
]
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"output_type": "stream",
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"text": [
"00:32 1.1Gb 99.7% Searching, 2.7% matched\r"
]
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 100.0% Searching, 2.7% matched\r",
"\r\n"
]
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"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
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"text": [
"00:02 1.1Gb Database loaded\r\n",
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]
},
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"text": [
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"text": [
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"text": [
"00:23 1.1Gb 65.8% Searching, 2.2% matched\r"
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"text": [
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"text": [
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"text": [
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"text": [
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"text": [
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"text": [
"00:35 1.1Gb 100.0% Searching, 2.3% matched\r",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
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]
},
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"text": [
"00:28 1.1Gb 100.0% Searching, 2.9% matched\r",
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]
},
{
"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
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"text": [
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"text": [
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"00:03 1.1Gb 2.5% Searching, 1.3% matched\r"
]
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]
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]
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{
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"stream": "stdout",
"text": [
"00:31 1.1Gb 100.0% Searching, 2.9% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
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"0"
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"00:04 1.1Gb 5.9% Searching, 3.3% matched\r"
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"stream": "stdout",
"text": [
"00:10 1.1Gb 28.2% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 30.6% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 34.2% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 37.5% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 41.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 46.8% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 50.9% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 54.2% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 58.1% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 61.1% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 63.8% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 66.5% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 70.3% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 74.7% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 76.7% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 81.2% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 84.3% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 88.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 91.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 93.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 95.9% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 99.4% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 100.0% Searching, 4.5% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.9% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.7% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 10.7% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.6% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.0% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.2% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 19.7% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:12 1.1Gb 21.0% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(44300,0xb0103000) malloc: *** mmap(size=1123594240) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1123590396), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-06.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-06.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123590396), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.2% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.8% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:05 1.1Gb 6.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.3% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.6% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.1% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 13.3% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 15.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 17.1% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 19.2% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 20.9% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 23.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 24.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 27.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 28.7% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 30.4% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 32.8% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 35.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 36.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 38.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 39.6% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 40.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 43.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 44.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 46.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 48.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 50.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 51.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 53.4% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 55.0% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 56.1% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 58.6% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 60.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 62.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 64.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 65.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:39 1.1Gb 67.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 69.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 70.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 73.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 74.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 76.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 78.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 80.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 83.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 85.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 86.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:50 1.1Gb 88.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 90.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:52 1.1Gb 92.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:53 1.1Gb 93.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:54 1.1Gb 95.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:55 1.1Gb 97.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:56 1.1Gb 99.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:56 1.1Gb 100.0% Searching, 4.0% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.7% Searching, 2.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.2% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 4.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 6.2% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 7.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 9.8% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 12.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 13.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 14.5% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 16.1% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 17.6% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 19.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 21.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 24.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 25.7% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 27.3% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 28.9% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 30.1% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 31.9% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 32.9% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 34.3% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 36.4% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 38.5% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 40.6% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 42.4% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 45.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 47.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 48.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 50.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 51.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 52.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 54.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 56.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 57.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 59.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 61.6% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 63.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 64.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 66.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 68.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 71.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 73.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 75.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 77.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 79.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 81.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 84.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:50 1.1Gb 86.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 88.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:52 1.1Gb 90.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:53 1.1Gb 92.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:54 1.1Gb 95.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:55 1.1Gb 96.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:56 1.1Gb 97.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:57 1.1Gb 99.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:57 1.1Gb 100.0% Searching, 4.3% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.6% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:04 1.1Gb 3.0% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:05 1.1Gb 4.9% Searching, 3.3% matched\r"
]
},
{
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"text": [
"00:06 1.1Gb 6.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:07 1.1Gb 8.5% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:08 1.1Gb 10.9% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:09 1.1Gb 12.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:10 1.1Gb 14.5% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 16.9% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 18.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 20.7% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 23.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:15 1.1Gb 25.4% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 28.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 30.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 32.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 34.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 37.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 39.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 41.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:23 1.1Gb 43.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:24 1.1Gb 44.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:25 1.1Gb 47.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 49.2% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 51.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 53.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 55.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 57.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 59.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 62.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 64.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 66.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 68.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 70.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 72.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 75.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 77.5% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 79.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 82.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 84.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 85.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 87.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 88.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 91.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 94.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 95.5% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 98.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 100.0% Searching, 4.2% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(46222,0xac31a2c0) malloc: *** mmap(size=1182121984) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1182121920), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-10.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-10.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1182121920), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.0% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.1% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.6% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 9.0% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 10.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 13.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.2% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 21.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 24.3% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 26.7% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 29.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 31.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 33.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 35.9% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 37.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 40.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 43.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 45.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 47.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 49.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 51.3% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 53.4% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 55.7% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 58.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 60.6% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 63.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 65.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 67.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 69.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 71.5% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 73.1% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 75.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 78.1% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 80.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 82.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 85.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 87.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 89.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 91.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 93.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
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"text": [
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"text": [
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"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.5Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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},
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"text": [
"00:20 1.1Gb 100.0% Searching, 3.1% matched\r",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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"text": [
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"output_type": "stream",
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"text": [
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"text": [
"00:27 1.1Gb 100.0% Searching, 3.6% matched\r",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
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"text": [
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]
},
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"00:12 1.1Gb 38.9% Searching, 3.7% matched\r"
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"00:13 1.1Gb 42.8% Searching, 3.8% matched\r"
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{
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]
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]
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"00:19 1.1Gb 66.6% Searching, 3.8% matc"
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},
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{
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"00:22 1.1Gb 78.6% Searching, 3.7% matched\r"
]
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{
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"text": [
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"00:24 1.1Gb 86.9% Searching, 3.6% matched\r"
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"text": [
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{
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"00:26 1.1Gb 94.1% Searching, 3.7% matched\r"
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]
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"text": [
"00:27 1.1Gb 100.0% Searching, 3.6% matched\r",
"\r\n"
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},
{
"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
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]
},
{
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"text": [
"00:03 1.1Gb 1.4% Searching, 2"
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},
{
"output_type": "stream",
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"text": [
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{
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"00:04 1.1Gb 5.8% Searching, 1.9% matched\r"
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"00:11 1.1Gb 30.3% Searching, 3.8% matched\r"
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"00:13 1.1Gb 38.9% Searching, 3.7% matched\r"
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]
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"text": [
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"text": [
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"text": [
"00:30 1.1Gb 100.0% Searching, 3.4% matched\r",
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"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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"text": [
"00:31 1.1Gb 100.0% Searching, 3.4% matched\r",
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"http://drive5.com/usearch\r\n",
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"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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"00:31 1.1Gb 100.0% Searching, 4.0% matched\r",
"\r\n"
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},
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"output_type": "stream",
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"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"\r\n"
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},
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},
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"stream": "stdout",
"text": [
"00:07 1.1Gb 14.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 17.3% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 19.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 23.0% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 24.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 27.7% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 30.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 33.6% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 36.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 39.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 43.2% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 45.3% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 48.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 51.2% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 53.3% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 55.8% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 57.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 61.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 63.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 66.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 69.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 72.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 75.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 77.8% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 80.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 82.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 85.1% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 87.8% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 90.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 93.4% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 96.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 99.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 100.0% Searching, 3.4% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.7% Searching, 12.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.6% Searching, 6.4% matched \r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.3% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.1% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.3% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.2% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.7% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.8% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 23.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 26.9% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 29.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 32.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 35.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 37.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 40.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 42.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 45.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 47.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 51.0% Searching, 4.0% m"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"atched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 54.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 57.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 59.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 62.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 65.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 67.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(49735,0xb0103000) malloc: *** mmap(size=1123459072) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1123456320), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-21.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-21.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123456320), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.3% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.9% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 7.3% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 10.1% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 13.0% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 15.2% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 18.3% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 20.4% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 22.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 25.7% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 28.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 31.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 34.4% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 37.7% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 40.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 43.6% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 46.7% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 49.6% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 51.9% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 54.0% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 56.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 59.1% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:25 1.1Gb 61.9% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 65.0% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 68.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 71.5% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 74.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 76.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 79.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 82.2% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 84.3% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:34 1.1Gb 86.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 87.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 89.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 92.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 95.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 98.0% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 100.0% Searching, 3.2% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb Database loaded\r\n",
"00:03 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.5% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 7.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 9.8% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 13.0% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(50453,0xb0185000) malloc: *** mmap(size=1097928704) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1097928221), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-23.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-23.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1097928221), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.8% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 5.6% Searching, 2.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 9.5% Searching, 1.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 13.1% Searching, 2.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 16.5% Searching, 2.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
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"text": [
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{
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"text": [
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"Licensed to: sr320@uw.edu\r\n",
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"text": [
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"00:00 1.6Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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"text": [
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"text": [
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},
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"text": [
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]
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]
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]
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},
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]
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]
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"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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]
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{
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"text": [
"00:59 1.1Gb 100.0% Searching, 4.1% matched\r",
"\r\n"
]
},
{
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
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"text": [
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]
},
{
"output_type": "stream",
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"text": [
"00:03 1.1Gb Database loaded\r\n",
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},
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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"01:11 1.1Gb 100.0% Searching, 4.1% matched\r",
"\r\n"
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
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"text": [
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},
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]
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]
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"00:43 1.1Gb 61.9% Searching, 3.9% matched\r"
]
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]
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]
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]
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"00:49 1.1Gb 72.0% Searching, 3.9% matched\r"
]
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]
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"00:51 1.1Gb 75.4% Searching, 3.9% matched\r"
]
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"00:52 1.1Gb 77.1% Searching, 4.0% matched\r"
]
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"00:53 1.1Gb 78.5% Searching, 4.0% matched\r"
]
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]
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"text": [
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]
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]
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]
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"text": [
"00:59 1.1Gb 90.6% Search"
]
},
{
"output_type": "stream",
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"text": [
"ing, 3.9% matched\r"
]
},
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"output_type": "stream",
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"text": [
"01:00 1.1Gb 92.3% Searching, 3.9% matched\r"
]
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},
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"output_type": "stream",
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"text": [
"01:03 1.1Gb 100.0% Searching, 3.9% matched\r",
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]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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},
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"text": [
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]
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"text": [
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"text": [
"00:52 1.1Gb 99.1% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:52 1.1Gb 100.0% Searching, 3.4% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
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"text": [
"00:00 1.8Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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},
{
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},
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},
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]
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{
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"text": [
"00:37 1.1Gb 100.0% Searching, 3.8% matched\r",
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},
{
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
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"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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},
{
"output_type": "stream",
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"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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},
{
"output_type": "stream",
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"00:02 1.1Gb Database loaded\r\n",
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},
{
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"text": [
"g, 3.0% matched\r"
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 19.6% Searching, 3.2% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:11 1.1Gb 21.9% Searching, 3.2% matched\r"
]
},
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"00:12 1.1Gb 23.5% Searching, 3.2% matched\r"
]
},
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"00:13 1.1Gb 26.0% Searching, 3.3% matched\r"
]
},
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"text": [
"00:14 1.1Gb 28.7% Searching, 3.3% matched\r"
]
},
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"00:15 1.1Gb 31.0% Searching, 3.4% matched\r"
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},
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"00:16 1.1Gb 34.6% Searching, 3.2% matched\r"
]
},
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"00:17 1.1Gb 37.0% Searching, 3.2% matched\r"
]
},
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"text": [
"00:18 1.1Gb 39.6% Searching, 3.2% matched\r"
]
},
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"text": [
"00:19 1.1Gb 42.3% Searching, 3.3% matched\r"
]
},
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"text": [
"00:20 1.1Gb 46.7% Searching, 3.4% matched\r"
]
},
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"00:21 1.1Gb 48.0% Searching, 3.5% matched\r"
]
},
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"00:22 1.1Gb 50.9% Searching, 3.5% matched\r"
]
},
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"text": [
"00:23 1.1Gb 53.3% Searching, 3.4% matched\r"
]
},
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"00:24 1.1Gb 56.3% Searching, 3.4% matched\r"
]
},
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"00:25 1.1Gb 58.0% Searching, 3.5% matched\r"
]
},
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"text": [
"00:26 1.1Gb 60.7% Searching, 3.5% matched\r"
]
},
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"00:27 1.1Gb 63.5% Searching, 3.4% matched\r"
]
},
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"00:28 1.1Gb 66.3% Searching, 3.5% matched\r"
]
},
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"00:29 1.1Gb 69.4% Searching, 3.6% matched\r"
]
},
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"00:30 1.1Gb 71.7% Searching, 3.6% matched\r"
]
},
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"00:31 1.1Gb 74.9% Searching, 3.5% matched\r"
]
},
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"text": [
"00:32 1.1Gb 78.8% Searching, 3.5% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:33 1.1Gb 80.7% Searching, 3.5% matched\r"
]
},
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]
},
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"output_type": "stream",
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"text": [
"00:35 1.1Gb 85.9% Searching, 3.5% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:36 1.1Gb 88.3% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:37 1.1Gb 90.1% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:38 1.1Gb 93.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 95.3% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:40 1.1Gb 98.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 99.8% Searching, 3.6% matched\r",
"00:41 1.1Gb 100.0% Searching, 3.6% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.1% Searching, 1.2% matched\r"
]
},
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"00:04 1.1Gb 3.1% Searching, 2.7% matched\r"
]
},
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"00:05 1.1Gb 5.0% Searching, 4.3% matched\r"
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},
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"00:06 1.1Gb 6.0% Searching, 4.1% matched\r"
]
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"00:07 1.1Gb 7.9% Searching, 4.3% matched\r"
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"00:09 1.1Gb 12.9% Searching, 3.6% matched\r"
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},
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"00:12 1.1Gb 20.1% Searching, 4.2% matched\r"
]
},
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"00:13 1.1Gb 22.7% Searching, 4.0% matched\r"
]
},
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"00:14 1.1Gb 24.6% Searching, 3.9% matched\r"
]
},
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]
},
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},
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},
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]
},
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"00:19 1.1Gb 36.0% Searching, 3.7% matched\r"
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},
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},
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]
},
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"00:22 1.1Gb 42.3% Searching, 3.7% matched\r"
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},
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},
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]
},
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},
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},
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},
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]
},
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]
},
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"00:44 1.1Gb 84.9% Searching, 3.7% matched\r"
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},
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"00:45 1.1Gb 86.5% Searching, 3.7% matched\r"
]
},
{
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"00:46 1.1Gb 88.5% Searching, 3.7% matched\r"
]
},
{
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"text": [
"00:47 1.1Gb 90.3% Searching, 3.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:48 1.1Gb 92.8% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:49 1.1Gb 94.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:50 1.1Gb 95.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 98.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 100.0% Searching, 3.7% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.9% Searching, 4.5% matched\r"
]
},
{
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"00:04 1.1Gb 4.1% Searching, 3.8% matched\r"
]
},
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"00:05 1.1Gb 5.9% Searching, 3.7% matched\r"
]
},
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"00:06 1.1Gb 8.0% Searching, 4.0% matched\r"
]
},
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"00:07 1.1Gb 10.8% Searching, 3.3% matched\r"
]
},
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"00:08 1.1Gb 13.2% Searching, 3.3% matched\r"
]
},
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"00:09 1.1Gb 14.9% Searching, 3.6% matched\r"
]
},
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]
},
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]
},
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"00:12 1.1Gb 20.1% Searching, 3.6% matched\r"
]
},
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"00:13 1.1Gb 22.3% Searching, 3.6% matched\r"
]
},
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"00:14 1.1Gb 24.3% Searching, 3.5% matched\r"
]
},
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"00:15 1.1Gb 26.7% Searching, 3.5% matched\r"
]
},
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"00:16 1.1Gb 29.4% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"00:17 1.1Gb 31.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:18 1.1Gb 33.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:19 1.1Gb 35.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:20 1.1Gb 37.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:21 1.1Gb 39.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:22 1.1Gb 41.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"00:23 1.1Gb 43.2% Searching, 3.8% matched\r"
]
},
{
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"00:24 1.1Gb 45.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:25 1.1Gb 47.3% Searching, 4.0% matched\r"
]
},
{
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"00:26 1.1Gb 49.6% Searching, 3.9% matched\r"
]
},
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"00:27 1.1Gb 51.8% Searching, 3.9% matched\r"
]
},
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"00:28 1.1Gb 54.5% Searching, 3.8% matched\r"
]
},
{
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"00:29 1.1Gb 57.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:30 1.1Gb 59.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 61.7% Searchi"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"ng, 3.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:32 1.1Gb 63.5% Searching, 3.8% matched\r"
]
},
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"00:33 1.1Gb 65.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:34 1.1Gb 67.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:35 1.1Gb 69.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:36 1.1Gb 71.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:37 1.1Gb 73.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 75.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 78.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 80.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 82.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 84.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 86.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 88.7% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(57251,0xb0081000) malloc: *** mmap(size=1123725312) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1123724480), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-37.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-37.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123724480), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.5% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.6% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.0% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.7% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 11.6% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 14.1% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 16.4% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 18.7% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.8% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 23.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 25.8% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 28.3% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 31.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 34.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 36.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 39.2% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(57744,0xb0103000) malloc: *** mmap(size=1182121984) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1182121920), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-38.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-38.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1182121920), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(57931,0xb0185000) malloc: *** mmap(size=1180405760) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1180403445), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-39.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-39.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1180403445), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.1% Searching, 1.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.2% Searching, 2.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.4% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.5% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 10.7% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 13.3% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.9% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.8% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 22.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 24.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 26.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 27.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 29.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 31.8% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 34.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 36.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 38.6% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 41.1% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 43.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 46.0% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 48.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 50.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 53.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 55.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 57.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 59.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 62.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 63.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 66.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 68.1% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 70.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 74.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 77.3% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 79.8% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 82.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 84.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 86.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 88.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 93.2% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 95.6% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 98.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:47 1.1Gb 99.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 100.0% Searching, 4.3% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.8% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 4.1% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 6.6% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 8.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(58493,0xb0103000) malloc: *** mmap(size=1123659776) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Out of memory mymalloc(1123657437), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-41.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-41.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123657437), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.4% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.0% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.0% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.3% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.5% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.2% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.3% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.2% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 19.0% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 21.4% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 23.5% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 24.9% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 27.3% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 28.6% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 31.0% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 32.7% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 35.1% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 37.4% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 39.8% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 41.7% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 43.5% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 45.5% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 47.8% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 50.1% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 52.8% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 54.8% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 57.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 59.2% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 61.1% Searching, 3.1% matched\r"
]
},
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"text": [
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"00:37 1.1Gb 74.5% Searching, 3.2% matched\r"
]
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"00:38 1.1Gb 76.4% Searching, 3.2% matched\r"
]
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"text": [
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]
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"text": [
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"text": [
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]
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"text": [
"00:49 1.1Gb 100.0% Searching, 3.4% matched\r",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
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},
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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},
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"00:31 1.1Gb 55.8% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:32 1.1Gb 58.3% Searching, 5.1% matched\r"
]
},
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"output_type": "stream",
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"00:33 1.1Gb 60.5% Searching, 5.1% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:34 1.1Gb 62.7% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:35 1.1Gb 64.0% Searching, 5.0% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:36 1.1Gb 66.7% Searching, 4.9% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:37 1.1Gb 69.4% Searching, 4.9% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:38 1.1Gb 72.2% Searching, 4.9% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:39 1.1Gb 73.9% Searching, 4.9% matched\r"
]
},
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"text": [
"00:40 1.1Gb 76.4% Searching, 4.9% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:41 1.1Gb 78.8% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:42 1.1Gb 80.5% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:43 1.1Gb 82.6% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:44 1.1Gb 84.3% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"00:45 1.1Gb 86.7% Searching, 4.8% matched\r"
]
},
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"00:46 1.1Gb 89.0% Searching, 4.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:47 1.1Gb 90.8% Searching, 4.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:48 1.1Gb 93.0% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:49 1.1Gb 94.9% Searching, 4.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:50 1.1Gb 98.0% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 99.8% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 100.0% Searching, 4.7% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.8% Searching, 4.7% matched\r"
]
},
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"00:04 1.1Gb 3.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:05 1.1Gb 5.8% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:06 1.1Gb 8.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:08 1.1Gb 11.4% Searching, 3.4% matched\r"
]
},
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"00:09 1.1Gb 13.9% Searching, 3.4% matched\r"
]
},
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"00:10 1.1Gb 16.8% Searching, 3.2% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:11 1.1Gb 18.7% Searching, 3.3% matched\r"
]
},
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"00:12 1.1Gb 20.0% Searching, 3.3% matched\r"
]
},
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"text": [
"00:13 1.1Gb 22.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 24.8% Searching, 3.3% matched\r"
]
},
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"output_type": "stream",
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"00:15 1.1Gb 27.7% Searching, 3.3% matched\r"
]
},
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"00:16 1.1Gb 29.0% Searching, 3.3% matched\r"
]
},
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"text": [
"00:17 1.1Gb 31.2% Searching, 3.3% matched\r"
]
},
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"output_type": "stream",
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"00:18 1.1Gb 33.2% Searching, 3.4% matched\r"
]
},
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"00:19 1.1Gb 35.9% Searching, 3.4% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:20 1.1Gb 36.9% Searching, 3.4% matched\r"
]
},
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"00:21 1.1Gb 39.3% Searching, 3.4% matched\r"
]
},
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"00:22 1.1Gb 41.1% Searching, 3.4% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:23 1.1Gb 43.3% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
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"00:24 1.1Gb 46.0% Searching, 3.3% matched\r"
]
},
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"output_type": "stream",
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"00:25 1.1Gb 47.3% Searching, 3.3% matched\r"
]
},
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"00:26 1.1Gb 49.8% Searching, 3.3% matched\r"
]
},
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"00:27 1.1Gb 52.2% Searching, 3.3% matched\r"
]
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"00:28 1.1Gb 54.3% Searching, 3.3% matched\r"
]
},
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"00:29 1.1Gb 56.1% Searching, 3.3% matched\r"
]
},
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"00:30 1.1Gb 57.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"0"
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},
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"text": [
"0:31 1.1Gb 60.7% Searching, 3.2% matched\r"
]
},
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"00:32 1.1Gb 62.7% Searching, 3.2% matched\r"
]
},
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"00:33 1.1Gb 65.6% Searching, 3.2% matched\r"
]
},
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"00:34 1.1Gb 67.4% Searching, 3.3% matched\r"
]
},
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"00:35 1.1Gb 69.4% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
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]
},
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"output_type": "stream",
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"00:37 1.1Gb 73.4% Searching, 3.4% matched\r"
]
},
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]
},
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]
},
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"00:40 1.1Gb 79.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:41 1.1Gb 82.0% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 84.0% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:43 1.1Gb 86.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 89.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 92.3% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 93.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 95.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 99.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 99.8% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 100.0% Searching, 3.7% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.8% Searching, 1.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:04 1.1Gb 3.1% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
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"00:05 1.1Gb 5.2% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:06 1.1Gb 7.2% Searching, 2.8% matched\r"
]
},
{
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"00:07 1.1Gb 9.4% Searching, 3.5% matched\r"
]
},
{
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"00:08 1.1Gb 11.5% Searching, 3.6% matched\r"
]
},
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"00:09 1.1Gb 14.1% Searching, 3.4% matched\r"
]
},
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"00:10 1.1Gb 16.4% Searching, 3.2% matched\r"
]
},
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"00:11 1.1Gb 18.5% Searching, 3.3% matched\r"
]
},
{
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"00:12 1.1Gb 20.0% Searching, 3.0% matched\r"
]
},
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"00:13 1.1Gb 22.1% Searching, 3.1% matched\r"
]
},
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"00:14 1.1Gb 23.7% Searching, 3.4% matched\r"
]
},
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"00:15 1.1Gb 25.2% Searching, 3.4% matched\r"
]
},
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"text": [
"00:16 1.1Gb 27.4% Searching, 3.5% matched\r"
]
},
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"00:17 1.1Gb 30.0% Searching, 3.4% matched\r"
]
},
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"text": [
"00:18 1.1Gb 32.5% Searching, 3.4% matched\r"
]
},
{
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"text": [
"00:19 1.1Gb 34.7% Searching, 3.3% matched\r"
]
},
{
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"text": [
"00:20 1.1Gb 37.0% Searching, 3.3% matched\r"
]
},
{
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"text": [
"00:21 1.1Gb 38.8% Searching, 3.4% matched\r"
]
},
{
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"text": [
"00:22 1.1Gb 40.2% Searching, 3.3% matched\r"
]
},
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"00:23 1.1Gb 41.6% Searching, 3.4% matched\r"
]
},
{
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"00:24 1.1Gb 42.8% Searching, 3.4% matched\r"
]
},
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"00:25 1.1Gb 44.5% Searching, 3.4% matched\r"
]
},
{
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"00:26 1.1Gb 47.0% Searching, 3.4% matched\r"
]
},
{
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"text": [
"00:27 1.1Gb 49.1% Searching, 3.4% matched\r"
]
},
{
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"text": [
"00:28 1.1Gb 52.7% Searching, 3.4% matched\r"
]
},
{
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"00:29 1.1Gb 53.6% Searching, 3.5% matched\r"
]
},
{
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"00:30 1.1Gb 55.4% Searching, 3.5% matched\r"
]
},
{
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"text": [
"00:31 1.1Gb 57.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 60.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:33 1.1Gb 62.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 64.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 66.6% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:36 1.1Gb 69.1% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
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"00:37 1.1Gb 70.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:38 1.1Gb 73.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
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"00:39 1.1Gb 76.1% Searching, 3.5% matched\r"
]
},
{
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"text": [
"00:40 1.1Gb 77.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 80.1% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 82.0% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 84.1% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 86.8% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 89.0% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 90.5% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 93.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 94.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 96.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:50 1.1Gb 98.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:50 1.1Gb 100.0% Searching, 3.6% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.8Mb Reading /Volumes"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.7% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(61545,0xb0185000) malloc: *** mmap(size=1123594240) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1123590396), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-48.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-48.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123590396), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb Database loaded\r\n",
"00:03 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.2% Searching, 7.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.7% Searching, 6.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.9% Searching, 6.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 12.0% Searching, 5.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 15.4% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 18.9% Searching, "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 21.2% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 24.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 27.4% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 30.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 34.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 37.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 40.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 43.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 46.7% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 50.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 53.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 56.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 60.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 63.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 66.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:25 1.1Gb 69.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 73.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 74.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 77.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 79.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 83.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 85.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 87.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 90.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 94.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 98.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 99.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 100.0% Searching, 4.0% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.2% Searching, 5.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.2% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.2% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.3% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.2% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.3% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.2% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 16.4% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 18.2% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 20.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 22.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(61967,0xac31a2c0) malloc: *** mmap(size=1180405760) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1180403445), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-50.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-50.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1180403445), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.3% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.8% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 11.2% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.9% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.8% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 21.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 24.7% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 26.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 29.5% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 31.3% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 33.7% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 35.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 37.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 39.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 42.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 43.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 46.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 48.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 50.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 52.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 54.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 57.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 59.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 61.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 63.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 65.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 68.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 71.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 72.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 75.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 77.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 79.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 81.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 83.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 85.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 87.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 89.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 91.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 93.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 96.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 98.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 100.0% Searching, 3.8% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.7% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.7% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 10.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 16.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 18.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 20.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 22.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 24.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 25.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 27.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 29.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 31.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 34.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 35.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 37.6% Searching, 3.9% matched\r"
]
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]
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"text": [
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]
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"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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]
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"00:37 1.1Gb 100.0% Searching, 3.9% matched\r",
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},
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]
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]
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]
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"text": [
"00:41 1.1Gb 100.0% Searching, 4.3% matched\r",
"\r\n"
]
},
{
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"stream": "stdout",
"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
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"text": [
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},
{
"output_type": "stream",
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"text": [
"00:02 1.1Gb Database loaded\r\n",
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]
},
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]
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},
{
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"stream": "stdout",
"text": [
"00:22 1.1Gb 40.4% Searching, 3.5% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:23 1.1Gb 43.0% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"00:24 1.1Gb 45.5% Searching, 3.6% matched\r"
]
},
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"00:25 1.1Gb 46.7% Searching, 3.5% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:26 1.1Gb 48.6% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 50.5% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:28 1.1Gb 51.8% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:29 1.1Gb 54.1% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:30 1.1Gb 55.8% Searching, 3.8% matched\r"
]
},
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"00:31 1.1Gb 58.8% Searching, 3.7% matched\r"
]
},
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"text": [
"00:32 1.1Gb 60.9% Searching, 3.7% matched\r"
]
},
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"00:33 1.1Gb 62.8% Searching, 3.7% matched\r"
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},
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"00:34 1.1Gb 64.7% Searching, 3.7% matched\r"
]
},
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"text": [
"00:35 1.1Gb 67.1% Searching, 3.9% matched\r"
]
},
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]
},
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]
},
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},
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]
},
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]
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]
},
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]
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]
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"text": [
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]
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"output_type": "stream",
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"text": [
"00:45 1.1Gb 88.4% Searching, 3.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:46 1.1Gb 91.0% Searching, 3.8% matched\r"
]
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"output_type": "stream",
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"text": [
"00:47 1.1Gb 93.4% Searching, 3.8% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:48 1.1Gb 95.6% Searching, 3.8% matched\r"
]
},
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 98.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 100.0% Searching, 3.9% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.5% Searching, 5.1% matched\r"
]
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"00:04 1.1Gb 4.7% Searching, 2.7% matched\r"
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"00:05 1.1Gb 7.3% Searching, 2.6% matched\r"
]
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"00:06 1.1Gb 9.3% Searching, 2.7% matched\r"
]
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"00:07 1.1Gb 12.4% Searching, 2.9% matched\r"
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"00:13 1.1Gb 26.3% Searching, 3.2% matched\r"
]
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"text": [
"00:14 1.1Gb 28.6% Searching, 3.3% matched\r"
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"00:15 1.1Gb 30.6% Searching, 3.3% matched\r"
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]
},
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"00:32 1.1Gb 68.5% Searching, 3.2% matched\r"
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},
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},
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},
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},
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]
},
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"output_type": "stream",
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"text": [
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},
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"output_type": "stream",
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"text": [
"00:46 1.1Gb 100.0% Searching, 3.4% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:03 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
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"stream": "stdout",
"text": [
"00:04 1.1Gb 3.2% Searching, 1.9% matched\r"
]
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"00:05 1.1Gb 5.7% Searching, 2.2% matched\r"
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"00:06 1.1Gb 8.7% Searching, 2.3% matched\r"
]
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]
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]
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"00:18 1.1Gb 36.1% Searching, 3.5% matched\r"
]
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"text": [
"00:19 1.1Gb 37.7% Searching, 3.5% matched\r"
]
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{
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"00:20 1.1Gb 40.1% Searching, 3.6% matched\r"
]
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"text": [
"00:21 1.1Gb 41.8% Searching, 3.6% matched\r"
]
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{
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"text": [
"00:22 1.1Gb 44.1% Searching, 3.6% "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"matched\r"
]
},
{
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"text": [
"00:23 1.1Gb 46.4% Searching, 3.6% matched\r"
]
},
{
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"00:24 1.1Gb 49.0% Searching, 3.5% matched\r"
]
},
{
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]
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{
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]
},
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"00:27 1.1Gb 56.2% Searching, 3.5% matched\r"
]
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{
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"00:28 1.1Gb 58.1% Searching, 3.5% matched\r"
]
},
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]
},
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"00:30 1.1Gb 62.3% Searching, 3.6% matched\r"
]
},
{
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"00:31 1.1Gb 64.2% Searching, 3.5% matched\r"
]
},
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"00:32 1.1Gb 66.0% Searching, 3.5% matched\r"
]
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},
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"00:34 1.1Gb 69.2% Searching, 3.7% matched\r"
]
},
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]
},
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"00:36 1.1Gb 73.0% Searching, 3.6% matched\r"
]
},
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"output_type": "stream",
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"00:37 1.1Gb 75.4% Searching, 3.6% matched\r"
]
},
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},
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]
},
{
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]
},
{
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]
},
{
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"00:42 1.1Gb 86.1% Searching, 3.7% matched\r"
]
},
{
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"00:43 1.1Gb 87.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"00:44 1.1Gb 89.5% Searching, 3.7% matched\r"
]
},
{
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"text": [
"00:45 1.1Gb 92.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 94.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:47 1.1Gb 96.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 98.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 100.0% Searching, 3.7% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n"
]
},
{
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"text": [
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
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"text": [
"00:03 1.1Gb 1.4% Searching, 5.0% matched\r"
]
},
{
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"text": [
"00:04 1.1Gb 4.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(65564,0xb0081000) malloc: *** mmap(size=1189081088) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1189077285), curr 1.06e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-58.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-58.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1189077285), curr 1.06e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.5% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.4% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.2% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.0% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 16.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 19.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 21.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 23.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 26.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 28.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 31.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 33.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 35.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 37.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 39.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 40.4% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 42.7% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 44.5% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 46.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 48.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 50.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 51.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 54.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 55.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:30 1.1Gb 58.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 60.4% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 62.3% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 65.1% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 67.5% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 68.9% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 70.8% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 73.2% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 75.9% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 78.8% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 82.4% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 83.1% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 87.3% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 89.7% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 92.6% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 95.7% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 98.0% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 99.8% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 100.0% Searching, 4.4% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.3% Searching, 5.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.6% Searching, 5.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.6% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.9% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.0% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 13.9% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 15.5% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 17.2% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 18.8% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 20.5% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 22.9% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 25.3% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 27.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 30.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 32.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 35.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 37.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 38.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 41.1% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 43.1% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 44.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 46.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 49.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 52.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 54.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 56.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 58.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 60.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 63.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 65.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 67.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 69.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 71.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 73.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 75.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 77.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 80.0% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 82.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 84.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 86.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 88.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 90.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 92.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 95.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 97.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 99.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 100.0% Searching, 3.7% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.4% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.5% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.4% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.1% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.8% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 13.0% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 18.4% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 22.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 24.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 26.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 29.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 31.5% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 33.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 35.3% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 37.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 40.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 42.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 44.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 46.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 48.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 50.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 53.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 55.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 57.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:29 1.1Gb 59.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 63.5% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 63.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 65.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 68.4% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 71.5% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 73.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 75.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 78.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 80.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 82.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 84.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 86.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 89.0% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 91.4% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 93.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 95.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 98.0% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 99.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 100.0% Searching, 3.8% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.8% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.3% Searching, 5.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.5% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 9.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 11.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 14.7% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 17.4% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 20.2% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 22.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 25.0% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 27.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 30.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 32.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 34.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 37.8% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 40.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 42.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 45.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 47.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 50.0% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 52.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 55.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 57.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 59.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 62.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 65.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 67.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 70.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 73.0% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 75.7% Searching, 3.6% ma"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"tched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 78.3% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 80.5% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 83.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 85.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 87.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 91.0% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 93.3% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 95.7% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 99.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 100.0% Searching, 3.6% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r",
"00:03 1.1Gb 0.6% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:04 1.1Gb 4.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 7.7% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 11.2% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 14.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 18.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 22.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 24.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 27.0% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(67617,0xb0081000) malloc: *** mmap(size=1120374784) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1120374780), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-63.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-63.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1120374780), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.0% Searching, 5.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.8% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 7.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 9.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 12.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 13.8% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.0% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.2% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 18.2% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 19.9% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 21.9% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 24.1% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 25.8% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(67747,0xb0185000) malloc: *** mmap(size=1216057344) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1216056380), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-64.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-64.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1216056380), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.3% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.7% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 8.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 10.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 12.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 15.0% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 17.6% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 20.1% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 22.4% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 24.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 27.0% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 29.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 31.1% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 33.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 35.3% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 38.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 40.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 43.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 46.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 48.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 50.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 53.2% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 55.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 57.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 60.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 62.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 65.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 68.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 70.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 72.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 75.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 76.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 79.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 80.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 82.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 85.8% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 88.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 90.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 92.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 94.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 97.1% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 99.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 100.0% Searching, 3.6% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:01 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb Database loaded\r\n",
"00:03 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 2.4% Searching, 2.1% matched\r"
]
},
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"00:05 1.1Gb 4.5% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:06 1.1Gb 6.5% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:07 1.1Gb 10.3% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:08 1.1Gb 11.8% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:09 1.1Gb 14.6% Searching, 2.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:10 1.1Gb 17.2% Searching, 2.4% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:11 1.1Gb 20.6% Searching, 2.3% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:12 1.1Gb 21.8% Searching, 2.3% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:13 1.1Gb 24.8% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:14 1.1Gb 26.9% Searching, 2.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 29.4% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 32.2% Searching, 2.6% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:17 1.1Gb 34.3% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:18 1.1Gb 36.5% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:19 1.1Gb 38.4% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:20 1.1Gb 40.9% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:21 1.1Gb 42.8% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:22 1.1Gb 45.0% Searching, 2.7% matched\r"
]
},
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"text": [
"00:23 1.1Gb 46.9% Searching, 2.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:24 1.1Gb 49.2% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:25 1.1Gb 50.8% Searching, 2.7% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:26 1.1Gb 53.1% Searching, 2.9% matched\r"
]
},
{
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"00:27 1.1Gb 55.2% Searching, 2.9% matched\r"
]
},
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"text": [
"00:28 1.1Gb 57.2% Searching, 2.9% matched\r"
]
},
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"00:29 1.1Gb 59.1% Searching, 3.0% matched\r"
]
},
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"text": [
"00:30 1.1Gb 61.8% Searching, 3.0% matched\r"
]
},
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]
},
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"text": [
"00:32 1.1Gb 64.9% Searching, 3.0% matched\r"
]
},
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 67.6% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 69.3% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 71.2% Searching, 3.0% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:36 1.1Gb 73.4% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:37 1.1Gb 75.6% Searching, 3.1% matched\r"
]
},
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"output_type": "stream",
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"text": [
"00:38 1.1Gb 77.3% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 79.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 81.7% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 83.3% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 85.3% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 87.6% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 89.7% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:45 1.1Gb 92.1% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 93.9% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 95.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 98.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 100.0% Searching, 3.2% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.4% Searching, 1.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 5.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 8.3% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 11.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 14.0% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 16.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 19.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 22.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 25.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 27.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 29.9% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 32.4% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 34.8% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 38.5% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 40.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 43.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 45.9% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 48.5% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 51.7% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 53.7% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 56.1% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 58.9% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 61.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 63.7% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 66.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(68935,0xb0185000) malloc: *** mmap(size=1100185600) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1100182557), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-67.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-67.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1100182557), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.3% Searching, 1.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.2% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 8.3% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 11.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 14.3% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 17.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 22.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 24.4% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 27.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 31.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 34.7% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 38.1% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 41.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 45.2% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 48.4% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 51.8% Searching, 3.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 55.2% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 59.6% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 62.8% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 66.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 69.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 73.5% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 76.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 79.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 83.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 87.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 89.6% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 93.3% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 96.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 99.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 100.0% Searching, 3.8% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 2.7% Searching, 3.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 4.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.2% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.7% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.4% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 13.5% Searching, 5.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 14.9% Searching, 5.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 16.7% Searching, 5.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 19.1% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 20.9% Searching, 5.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 23.1% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 24.3% Searching, 5.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 26.7% Searching, 5.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 27.9% Searching, 5.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 30.1% Searching, 5.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 32.0% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 33.9% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 37.1% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 39.6% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 42.0% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 43.8% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:25 1.1Gb 46.1% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 48.5% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 50.5% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
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"text": [
"00:28 1.1Gb 52.2% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 53.8% Searching, 5.0% matched\r"
]
},
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 56.3% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 57.0% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 59.6% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 62.1% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 64.9% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 67.7% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 68.9% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 71.4% Searching, 5.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 73.8% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 75.9% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 77.9% Searching, 4.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 79.7% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 82.3% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 83.9% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 86.4% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 89.3% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 91.3% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 92.6% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 94.3% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:49 1.1Gb 96.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:50 1.1Gb 98.5% Searching, 4.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:51 1.1Gb 99.8% Searching, 4.6% matched\r",
"00:51 1.1Gb 100.0% Searching, 4.6% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.1Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.6% Searching, 6.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.4% Searching, 5.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 7.3% Searching, 5.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.4% Searching, 5.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.6% Searching, 4.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 14.1% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 16.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 19.2% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 21.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 23.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 25.4% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 27.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 29.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 31.3% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 33.9% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 36.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 38.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 40.6% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 42.2% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 44.5% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 46.4% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 49.4% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 50.9% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 52.8% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 55.3% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 57.5% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 59.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 61.5% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"0:32 1.1Gb 63.6% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 65.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 67.8% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 70.0% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 72.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 74.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 76.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 78.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 81.1% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 83.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 85.3% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 87.7% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:44 1.1Gb 89.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:45 1.1Gb 91.7% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:46 1.1Gb 93.8% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:47 1.1Gb 96.0% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(70150,0xb0185000) malloc: *** mmap(size=1121312768) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1121312192), curr 1.08e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-70.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-70.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1121312192), curr 1.08e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 0.7% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 5.4% Searching, 4.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 6.8% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 9.2% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 11.3% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 13.5% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 15.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 17.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 20.0% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 22.7% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 24.6% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 27.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 29.3% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 31.2% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 33.9% Searching, 3.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 36.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 38.4% Searching, 3.9% matched\r"
]
},
{
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]
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]
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"text": [
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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]
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"00:28 1.1Gb 83.0% Searching, 3.5% matched\r"
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]
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"00:30 1.1Gb 90.3% Searching, 3.4% matched\r"
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]
},
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"\r\n"
]
},
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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},
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},
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]
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]
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"00:31 1.1Gb 65.1% Searching, 3.9% matched\r"
]
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"00:32 1.1Gb 66.9% Searching, 3.9% matched\r"
]
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"00:33 1.1Gb 68.8% Searching, 3.8% matched\r"
]
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"00:34 1.1Gb 70.5% Searching, 3.7% matched\r"
]
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"00:35 1.1Gb 72.8% Searching, 3.7% matched\r"
]
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]
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]
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]
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]
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]
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]
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"text": [
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]
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"text": [
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]
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"text": [
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]
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"text": [
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]
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"output_type": "stream",
"stream": "stdout",
"text": [
"00:48 1.1Gb 100.0% Searching, 3.8% matched\r",
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]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
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},
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"text": [
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},
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"output_type": "stream",
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"00:02 1.1Gb Database loaded\r\n",
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},
{
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"text": [
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]
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]
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"text": [
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]
},
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"text": [
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},
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]
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},
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},
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]
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]
},
{
"output_type": "stream",
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"text": [
"00:46 1.1Gb 100.0% Searching, 4.0% matched\r",
"\r\n"
]
},
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"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
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"text": [
"00:00 2.0Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
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"text": [
"00:02 1.1Gb Database loaded\r\n",
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},
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]
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]
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]
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]
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]
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]
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]
},
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]
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]
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]
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"text": [
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]
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"text": [
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]
},
{
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"00:34 1.1Gb 78.1% Searching, 3.6% matched\r"
]
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]
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]
},
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]
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]
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]
},
{
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]
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]
},
{
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]
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"text": [
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"00:44 1.1Gb 100.0% Searching, 3.5% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n",
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
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"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
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"text": [
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},
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]
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"text": [
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"text": [
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"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
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"Licensed to: sr320@uw.edu\r\n",
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},
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"text": [
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},
{
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"\r\n"
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},
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},
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"text": [
"00:22 1.1Gb 46.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 48.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 49.9% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 52.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 54.6% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 56.4% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 59.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 61.0% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(74777,0xb0103000) malloc: *** mmap(size=1242636288) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1242632997), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-80.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-80.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1242632997), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.9Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 1.9% Searching, 0.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 3.5% Searching, 1.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 6.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 9.0% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 11.6% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 13.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 16.5% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 18.6% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 21.8% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 24.7% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 27.8% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 29.6% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 30.9% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 32.2% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 34.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 38.2% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 39.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 42.4% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 45.7% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 47.8% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 50.6% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 53.1% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 56.0% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 57.9% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:27 1.1Gb 59.4% Searching, 2.9% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:28 1.1Gb 60.9% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:29 1.1Gb 63.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:30 1.1Gb 66.2% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:31 1.1Gb 68.7% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:32 1.1Gb 71.4% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:33 1.1Gb 73.9% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:34 1.1Gb 76.4% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:35 1.1Gb 78.9% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:36 1.1Gb 81.5% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:37 1.1Gb 84.2% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:38 1.1Gb 85.6% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:39 1.1Gb 88.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:40 1.1Gb 90.7% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:41 1.1Gb 93.1% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:42 1.1Gb 95.4% Searching, 3.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 98.0% Searching, 3.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:43 1.1Gb 100.0% Searching, 3.3% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.7Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 3.2% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 6.0% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 7.7% Searching, 4.4% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 10.6% Searching, 4.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 14.5% Searching, 4.2% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 18.3% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 21.2% Searching, 4.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 24.7% Searching, 4.3% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:11 1.1Gb 28.8% Searching, 4.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:12 1.1Gb 32.6% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:13 1.1Gb 35.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:14 1.1Gb 39.0% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:15 1.1Gb 42.3% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:16 1.1Gb 44.5% Searching, 3.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:17 1.1Gb 47.2% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:18 1.1Gb 49.9% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:19 1.1Gb 53.7% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:20 1.1Gb 56.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:21 1.1Gb 60.9% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:22 1.1Gb 64.6% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:23 1.1Gb 68.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:24 1.1Gb 71.4% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:25 1.1Gb 74.1% Searching, 3.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:26 1.1Gb 78.1% Searching, 3.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch(75539,0xac31a2c0) malloc: *** mmap(size=1123594240) failed (error code=12)\r\n",
"*** error: can't allocate region\r\n",
"*** set a breakpoint in malloc_error_break to debug\r\n",
"\r\n",
"Out of memory mymalloc(1123590396), curr 1.07e+09 bytes\r\n",
"\r\n",
"myutils.cpp(2212): \r\n",
"\r\n",
"usearch -ublast cgigas.part-82.fa -db /Volumes/Bay3/usearch/uniprot_sprot.udb -evalue 1e-5 -accel 0.8 -top_hits_only -maxhits 1 -blast6out /Volumes/web/cnidarian/cgigas8_cgigas.part-82.fa_ublast_sprot.b6\r\n",
"\r\n",
"---Fatal error---\r\n",
"Out of memory, mymalloc(1123590396), curr 1.07e+09 bytes\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"usearch v7.0.1090_i86osx32, 4.0Gb RAM (15.0Gb total), 4 cores\r\n",
"(C) Copyright 2013 Robert C. Edgar, all rights reserved.\r\n",
"http://drive5.com/usearch\r\n",
"\r\n",
"Licensed to: sr320@uw.edu\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:00 1.2Mb Reading /Volumes/Bay3/usearch/uniprot_sprot.udb\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:02 1.1Gb Database loaded\r\n",
"00:02 1.1Gb 0.1% Searching, 0.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:03 1.1Gb 11.7% Searching, 0.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:04 1.1Gb 22.2% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:05 1.1Gb 33.8% Searching, 2.5% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:06 1.1Gb 46.9% Searching, 2.6% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:07 1.1Gb 59.6% Searching, 2.7% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:08 1.1Gb 72.8% Searching, 3.1% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:09 1.1Gb 83.6% Searching, 3.0% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 98.0% Searching, 2.8% matched\r"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"00:10 1.1Gb 100.0% Searching, 2.8% matched\r",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"CPU times: user 22.2 s, sys: 5.51 s, total: 27.7 s\n",
"Wall time: 51min 16s\n"
]
}
],
"prompt_number": 45
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%time\n",
"for i in (\"cgigas.part-01.fa\",\"cgigas.part-02.fa\",\"cgigas.part-03.fa\",\"cgigas.part-04.fa\",\"cgigas.part-05.fa\",\"cgigas.part-06.fa\",\"cgigas.part-07.fa\",\"cgigas.part-08.fa\",\"cgigas.part-09.fa\",\"cgigas.part-10.fa\",\"cgigas.part-11.fa\",\"cgigas.part-12.fa\",\"cgigas.part-13.fa\",\"cgigas.part-14.fa\",\"cgigas.part-15.fa\",\"cgigas.part-16.fa\",\"cgigas.part-17.fa\",\"cgigas.part-18.fa\",\"cgigas.part-19.fa\",\"cgigas.part-20.fa\",\"cgigas.part-21.fa\",\"cgigas.part-22.fa\",\"cgigas.part-23.fa\",\"cgigas.part-24.fa\",\"cgigas.part-25.fa\",\"cgigas.part-26.fa\",\"cgigas.part-27.fa\",\"cgigas.part-28.fa\",\"cgigas.part-29.fa\",\"cgigas.part-30.fa\",\"cgigas.part-31.fa\",\"cgigas.part-32.fa\",\"cgigas.part-33.fa\",\"cgigas.part-34.fa\",\"cgigas.part-35.fa\",\"cgigas.part-36.fa\",\"cgigas.part-37.fa\",\"cgigas.part-38.fa\",\"cgigas.part-39.fa\",\"cgigas.part-40.fa\",\"cgigas.part-41.fa\",\"cgigas.part-42.fa\",\"cgigas.part-43.fa\",\"cgigas.part-44.fa\",\"cgigas.part-45.fa\",\"cgigas.part-46.fa\",\"cgigas.part-47.fa\",\"cgigas.part-48.fa\",\"cgigas.part-49.fa\",\"cgigas.part-50.fa\",\"cgigas.part-51.fa\",\"cgigas.part-52.fa\",\"cgigas.part-53.fa\",\"cgigas.part-54.fa\",\"cgigas.part-55.fa\",\"cgigas.part-56.fa\",\"cgigas.part-57.fa\",\"cgigas.part-58.fa\",\"cgigas.part-59.fa\",\"cgigas.part-60.fa\",\"cgigas.part-61.fa\",\"cgigas.part-62.fa\",\"cgigas.part-63.fa\",\"cgigas.part-64.fa\",\"cgigas.part-65.fa\",\"cgigas.part-66.fa\",\"cgigas.part-67.fa\",\"cgigas.part-68.fa\",\"cgigas.part-69.fa\",\"cgigas.part-70.fa\",\"cgigas.part-71.fa\",\"cgigas.part-72.fa\",\"cgigas.part-73.fa\",\"cgigas.part-74.fa\",\"cgigas.part-75.fa\",\"cgigas.part-76.fa\",\"cgigas.part-77.fa\",\"cgigas.part-78.fa\",\"cgigas.part-79.fa\",\"cgigas.part-80.fa\",\"cgigas.part-81.fa\",\"cgigas.part-82.fa\",\"cgigas.part-83.fa\"):\n",
" !/Volumes/Bay3/Software/ncbi-blast-2.2.29+/bin/blastx \\\n",
"-query {i} \\\n",
"-db /Volumes/Bay3/Software/ncbi-blast-2.2.28+/db/uniprot_sprot \\\n",
"-evalue 1e-5 \\\n",
"-max_target_seqs 1 \\\n",
"-max_hsps 1 \\\n",
"-outfmt 6 \\\n",
"-num_threads 2 \\\n",
"-out /Volumes/Bay3/usearch/ncbi_{i}.results.b6"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"Split them up even more"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pwd"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!perl /Volumes/Bay3/Software/fasta-splitter.pl --part-size 1000 --measure count /Volumes/Bay3/usearch/cgigas.fa "
],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}