[info] Pulling image plugins/drone-git:latest Drone Git Plugin built from 43dcd64 $ git init Initialized empty Git repository in /drone/src/github.com/greenelab/continuous_analysis_rnaseq/.git/ $ git remote add origin https://github.com/greenelab/continuous_analysis_rnaseq.git $ git fetch --no-tags origin +refs/heads/staging: From https://github.com/greenelab/continuous_analysis_rnaseq * branch staging -> FETCH_HEAD * [new branch] staging -> origin/staging $ git reset --hard -q 494f61d15f1b18e82ab0aead397db24cc9ee1885 $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/refMrna.fa.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654626_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654626_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654628_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654628_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654633_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654633_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654636_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654636_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654637_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654637_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654639_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654639_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654641_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654641_2.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654643_1.fastq.gz $ wget -q ftp://ibi-admin-033.med.upenn.edu/rna/SRR1654643_2.fastq.gz $ mkdir -p kallisto_output $ kallisto index -i mm10 refMrna.fa.gz [build] loading fasta file refMrna.fa.gz [build] k-mer length: 31 [build] warning: clipped off poly-A tail (longer than 10) from 9710 target sequences [build] warning: replaced 24 non-ACGUT characters in the input sequence with pseudorandom nucleotides [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 174919 contigs and contains 64110878 k-mers $ kallisto quant -i mm10 -o kallisto_output/SRR1654626 --bootstrap-samples=10 SRR1654626_1.fastq.gz SRR1654626_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654626_1.fastq.gz SRR1654626_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 45,570,934 reads, 30,009,645 reads pseudoaligned [quant] estimated average fragment length: 168.039 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,168 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654628 --bootstrap-samples=10 SRR1654628_1.fastq.gz SRR1654628_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654628_1.fastq.gz SRR1654628_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 54,088,667 reads, 35,922,079 reads pseudoaligned [quant] estimated average fragment length: 175.781 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,351 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654633 --bootstrap-samples=10 SRR1654633_1.fastq.gz SRR1654633_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654633_1.fastq.gz SRR1654633_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 62,912,167 reads, 39,938,343 reads pseudoaligned [quant] estimated average fragment length: 168.12 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,190 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654636 --bootstrap-samples=10 SRR1654636_1.fastq.gz SRR1654636_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654636_1.fastq.gz SRR1654636_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 60,697,541 reads, 39,694,868 reads pseudoaligned [quant] estimated average fragment length: 154.954 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,098 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654637 --bootstrap-samples=10 SRR1654637_1.fastq.gz SRR1654637_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654637_1.fastq.gz SRR1654637_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 65,233,848 reads, 42,782,064 reads pseudoaligned [quant] estimated average fragment length: 157.66 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,108 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654639 --bootstrap-samples=10 SRR1654639_1.fastq.gz SRR1654639_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654639_1.fastq.gz SRR1654639_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 75,831,982 reads, 48,842,546 reads pseudoaligned [quant] estimated average fragment length: 150.127 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,111 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654641 --bootstrap-samples=10 SRR1654641_1.fastq.gz SRR1654641_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654641_1.fastq.gz SRR1654641_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 65,347,210 reads, 45,814,784 reads pseudoaligned [quant] estimated average fragment length: 156.027 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,128 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ kallisto quant -i mm10 -o kallisto_output/SRR1654643 --bootstrap-samples=10 SRR1654643_1.fastq.gz SRR1654643_2.fastq.gz -t 28 [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 35,026 [index] number of k-mers: 64,110,878 [index] number of equivalence classes: 81,212 [quant] running in paired-end mode [quant] will process pair 1: SRR1654643_1.fastq.gz SRR1654643_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 73,960,306 reads, 51,887,416 reads pseudoaligned [quant] estimated average fragment length: 160.683 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,181 rounds [~warn] number of threads (28) greater than number of bootstraps [~warn] (cont'd) updating threads to number of bootstraps 10 [bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 $ mkdir -p results $ Rscript r_script.r [1] "SRR1654626" "SRR1654628" "SRR1654633" "SRR1654636" "SRR1654637" [6] "SRR1654639" "SRR1654641" "SRR1654643" SRR1654626 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654626" SRR1654628 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654628" SRR1654633 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654633" SRR1654636 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654636" SRR1654637 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654637" SRR1654639 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654639" SRR1654641 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654641" SRR1654643 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654643" sample condition 1 mN5 mN 2 mN7 mN 3 mP1 mP 4 mP3 mP 5 mP5 mP 6 mT3 mT 7 mT5 mT 8 mT8 mT sample condition 1 mN5 mN 2 mN7 mN 3 mP1 mP 4 mP3 mP 5 mP5 mP 6 mT3 mT 7 mT5 mT 8 mT8 mT path 1 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654626 2 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654628 3 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654633 4 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654636 5 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654637 6 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654639 7 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654641 8 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654643 Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Loading required package: limma Loading required package: methods Attaching package: 'genefilter' The following object is masked from 'package:base': anyNA SRR1654626 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654626" SRR1654628 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654628" SRR1654633 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654633" SRR1654636 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654636" SRR1654637 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654637" SRR1654639 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654639" SRR1654641 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654641" SRR1654643 "/drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654643" [1] /drone/src/github.com/greenelab/continuous [2] analysis_rnaseq/kallisto_output/SRR1654626 [3] /drone/src/github.com/greenelab/continuous [4] analysis_rnaseq/kallisto_output/SRR1654628 [5] /drone/src/github.com/greenelab/continuous [6] analysis_rnaseq/kallisto_output/SRR1654633 [7] /drone/src/github.com/greenelab/continuous [8] analysis_rnaseq/kallisto_output/SRR1654636 [9] /drone/src/github.com/greenelab/continuous [10] analysis_rnaseq/kallisto_output/SRR1654637 [11] /drone/src/github.com/greenelab/continuous [12] analysis_rnaseq/kallisto_output/SRR1654639 [13] /drone/src/github.com/greenelab/continuous [14] analysis_rnaseq/kallisto_output/SRR1654641 [15] /drone/src/github.com/greenelab/continuous [16] analysis_rnaseq/kallisto_output/SRR1654643 9 Levels: /drone/src/github.com/greenelab/continuous ... FinalNames ActualNames Subtypes 1 /drone/src/github.com/greenelab/continuous mN5 mN 2 analysis_rnaseq/kallisto_output/SRR1654626 mN7 mN 3 /drone/src/github.com/greenelab/continuous mP1 mP 4 analysis_rnaseq/kallisto_output/SRR1654628 mP4 mP 5 /drone/src/github.com/greenelab/continuous mP5 mP 6 analysis_rnaseq/kallisto_output/SRR1654633 mT3 mT 7 /drone/src/github.com/greenelab/continuous mT5 mT 8 analysis_rnaseq/kallisto_output/SRR1654636 mT8 mT 9 /drone/src/github.com/greenelab/continuous mN5 mN 10 analysis_rnaseq/kallisto_output/SRR1654637 mN7 mN 11 /drone/src/github.com/greenelab/continuous mP1 mP 12 analysis_rnaseq/kallisto_output/SRR1654639 mP4 mP 13 /drone/src/github.com/greenelab/continuous mP5 mP 14 analysis_rnaseq/kallisto_output/SRR1654641 mT3 mT 15 /drone/src/github.com/greenelab/continuous mT5 mT 16 analysis_rnaseq/kallisto_output/SRR1654643 mT8 mT mN5 mN7 mP1 mP4 mP5 mT3 mT5 NM_001001130 108.657 118.3940 234.8120 175.344 169.448 277.2800 120.9100 NM_001001144 1458.840 1563.9800 1922.9200 2074.590 1955.750 1546.7800 1777.4600 NM_001001152 64.000 90.0000 142.0000 137.684 108.233 128.1770 73.1548 NM_001001160 0.000 0.0000 0.0000 0.000 0.000 0.0000 0.0000 NM_001001176 0.000 39.1487 78.5445 0.000 0.000 39.5625 0.0000 NM_001001177 2.000 0.0000 1.0000 0.000 0.000 0.0000 0.0000 mT8 NM_001001130 216.287 NM_001001144 2962.330 NM_001001152 149.884 NM_001001160 0.000 NM_001001176 157.569 NM_001001177 0.000 mN mP mT 1 1 0 0 2 1 0 0 3 0 1 0 4 0 1 0 5 0 1 0 6 0 0 1 7 0 0 1 8 0 0 1 attr(,"assign") [1] 1 1 1 attr(,"contrasts") attr(,"contrasts")$des [1] "contr.treatment" isexpr FALSE TRUE 7228 27798 [1] 27798 8 Warning message: In data.frame(pcCount$x, Names_count) : row names were found from a short variable and have been discarded [1] "#66C2A5" "#FC8D62" "#8DA0CB" mT.mN mT.mP mN.mP AveExpr F NM_008710 -7.4900342 -0.46334106 7.02669313 -0.07057568 421.12618 NM_146059 -6.5110115 -0.25868100 6.25233052 -4.88448742 126.95577 NM_001168516 6.9068855 7.17128107 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-1.11621632 67.99802 NM_016672 -5.0955476 -0.25853361 4.83701395 -5.23716252 67.85516 NM_001313976 -0.5712969 -6.23515949 -5.66386259 -4.12998991 66.88188 NM_001177752 -0.2020878 5.95591749 6.15800526 -2.57719338 65.09600 NR_045594 5.4772878 5.79005107 0.31276327 -4.09980322 64.92549 NM_009578 -5.0272456 -0.25853361 4.76871194 -5.25624286 63.32928 NM_001199244 -5.0092615 -0.25853361 4.75072789 -5.25763400 63.23773 NM_001013362 -6.8601913 0.50157296 7.36176427 -4.31161185 61.62473 NM_001278218 0.3604690 7.20604644 6.84557743 -1.93069926 59.26175 NM_026174 0.9798270 0.03596887 -0.94385811 6.81069840 58.93124 NM_001163540 -6.7133513 -0.23436029 6.47899098 -4.78387683 57.15645 NM_001039181 -5.8553704 -0.25853361 5.59683679 -5.05447440 55.05249 NM_011611 -4.6504257 -0.25853361 4.39189208 -5.34924257 53.25725 NM_001281862 -5.4036585 -0.25853361 5.14512489 -5.16651509 52.40912 NM_001291129 -4.8215033 -0.25853361 4.56296971 -5.30286492 52.30660 NM_001285855 -4.8620388 -4.81945046 0.04258837 -3.58442214 50.91381 NM_013822 -0.4208883 -1.12828837 -0.70740002 6.48798588 49.83866 NM_177192 1.2520316 0.47316631 -0.77886531 5.47849522 47.23033 NM_080453 -0.3827701 6.24012951 6.62289959 -2.36208139 46.86403 NM_010516 -1.2742250 -0.89593201 0.37829300 6.37826394 46.71247 NM_001281829 -6.4028773 -6.51061402 -0.10773675 -2.57050571 45.99589 NM_001311083 -5.0319043 -0.25853361 4.77337070 -5.25920464 45.84551 NM_021439 -1.0478988 2.28831354 3.33621231 0.66416634 45.75502 NM_133753 -0.7157280 -0.66147219 0.05425578 7.81104737 45.22813 NM_001122820 4.7113772 -0.27997201 -4.99134926 -2.39947920 45.04908 NM_007536 -3.3439208 -0.31497028 3.02895049 -1.20698573 43.50065 NM_001195421 5.0795593 0.82700326 -4.25255607 7.07465394 42.86202 NM_181541 1.4554747 -0.07677849 -1.53225319 3.47822791 42.79502 NM_029633 -7.5775869 -5.92310953 1.65447739 -1.65753360 42.27318 NM_178621 -0.2424468 4.43466763 4.67711438 -3.51538172 42.01963 NM_011723 -1.5421219 -0.22573386 1.31638805 4.92196561 41.09903 NM_007534 -4.5987268 0.92051267 5.51923946 -4.62026088 40.89074 NM_001270498 1.5361544 -0.53910255 -2.07525698 6.36689651 40.30004 NM_134069 -5.0212453 -4.31713709 0.70410823 -3.19912287 40.12031 NM_012048 -0.1225196 -0.95974746 -0.83722790 5.54000774 40.11746 NM_001113405 -2.0646522 -0.45422988 1.61042231 3.13413605 38.57954 NM_010439 0.2797116 0.55615641 0.27644482 9.39328577 38.51640 NM_177574 -4.0934565 -0.25853361 3.83492284 -5.48725503 38.18535 NM_177628 -2.1073933 -0.26672859 1.84066471 1.65543003 37.87948 NM_026014 0.2279928 0.89155158 0.66355878 5.18889222 37.75542 NM_001039059 -4.0494388 -0.25853361 3.79090515 -5.49848864 37.38716 NM_001316747 -0.8914811 4.19659697 5.08807807 -3.49428124 37.17094 NM_001270503 4.3836177 0.81366113 -3.56995653 0.08682260 37.07135 NM_011211 -0.9865150 1.40771576 2.39423077 2.50673928 36.86204 NM_001161433 -1.0268773 -1.47834535 -0.45146807 4.81419351 36.68323 NM_133786 0.2957088 0.84979383 0.55408503 7.86488034 36.60389 NM_007913 -1.8458978 -0.35661807 1.48927972 3.76912372 36.53853 NM_022032 0.3655713 -0.34408729 -0.70965860 7.68444490 36.46694 NM_001317354 -4.2108835 -0.25853361 3.95234990 -5.46142135 36.45922 NM_172881 1.4130628 -0.78932973 -2.20239258 5.24749714 36.40099 NM_001164528 -1.7773348 0.88526142 2.66259627 2.76796014 36.12473 P.Value adj.P.Val NM_008710 1.189433e-08 0.0003306385 NM_146059 1.159044e-06 0.0161095520 NM_001168516 2.046012e-06 0.0175288753 NM_001190718 3.199356e-06 0.0175288753 NM_001270499 5.035515e-06 0.0175288753 NM_001286824 5.404407e-06 0.0175288753 NM_153163 5.783860e-06 0.0175288753 NM_001111279 6.821370e-06 0.0175288753 NM_001130456 7.378019e-06 0.0175288753 NM_178634 7.852582e-06 0.0175288753 NM_009342 8.725527e-06 0.0175288753 NM_030696 8.761518e-06 0.0175288753 NM_001177774 8.898915e-06 0.0175288753 NM_001136484 9.850009e-06 0.0175288753 NM_173388 1.092697e-05 0.0175288753 NM_001271857 1.139385e-05 0.0175288753 NM_010598 1.151718e-05 0.0175288753 NM_008092 1.188874e-05 0.0175288753 NM_016672 1.198103e-05 0.0175288753 NM_001313976 1.263432e-05 0.0175604383 NM_001177752 1.395397e-05 0.0178018967 NR_045594 1.408885e-05 0.0178018967 NM_009578 1.543456e-05 0.0179720407 NM_001199244 1.551655e-05 0.0179720407 NM_001013362 1.705511e-05 0.0189639232 NM_001278218 1.967288e-05 0.0206716962 NM_026174 2.007827e-05 0.0206716962 NM_001163540 2.244429e-05 0.0222823702 NM_001039181 2.572257e-05 0.0246564117 NM_011611 2.900887e-05 0.0268796231 NM_001281862 3.074487e-05 0.0268975984 NM_001291129 3.096349e-05 0.0268975984 NM_001285855 3.413633e-05 0.0287552045 NM_013822 3.686929e-05 0.0301439018 NM_177192 4.473791e-05 0.0348390152 NM_080453 4.600613e-05 0.0348390152 NM_010516 4.654405e-05 0.0348390152 NM_001281829 4.919733e-05 0.0348390152 NM_001311083 4.977807e-05 0.0348390152 NM_021439 5.013169e-05 0.0348390152 NM_133753 5.225465e-05 0.0350795782 NM_001122820 5.300174e-05 0.0350795782 NM_007536 6.005752e-05 0.0388250920 NM_001195421 6.330994e-05 0.0393272801 NM_181541 6.366385e-05 0.0393272801 NM_029633 6.650732e-05 0.0401867697 NM_178621 6.794655e-05 0.0401867697 NM_011723 7.351293e-05 0.0424634434 NM_007534 7.485102e-05 0.0424634434 NM_001270498 7.881604e-05 0.0428168519 NM_134069 8.007461e-05 0.0428168519 NM_012048 8.009484e-05 0.0428168519 NM_001113405 9.197225e-05 0.0468268569 NM_010439 9.250574e-05 0.0468268569 NM_177574 9.536725e-05 0.0468268569 NM_177628 9.811080e-05 0.0468268569 NM_026014 9.925174e-05 0.0468268569 NM_001039059 1.027385e-04 0.0468268569 NM_001316747 1.048575e-04 0.0468268569 NM_001270503 1.058520e-04 0.0468268569 NM_011211 1.079811e-04 0.0468268569 NM_001161433 1.098428e-04 0.0468268569 NM_133786 1.106817e-04 0.0468268569 NM_007913 1.113789e-04 0.0468268569 NM_022032 1.121490e-04 0.0468268569 NM_001317354 1.122324e-04 0.0468268569 NM_172881 1.128642e-04 0.0468268569 NM_001164528 1.159235e-04 0.0473888489 mT-mN mT-mP mN-mP -1 45 3 14 0 27739 27788 27746 1 14 7 38 logFC t P.Value adj.P.Val B NR_004415 11.32 5.56 0.000593 0.110 -0.0344 NR_004416 11.32 5.56 0.000593 0.110 -0.0344 NR_027863 11.32 5.56 0.000593 0.110 -0.0344 NM_172519 8.57 3.37 0.010155 0.227 -2.3864 NM_001289443 7.89 3.54 0.008026 0.214 -2.1841 NM_001253770 7.86 5.00 0.001145 0.130 -0.5306 [1] 27798 Warning message: Removed 4 rows containing missing values (geom_point). logFC t P.Value adj.P.Val B NR_003278 16.51 1.65 1.40e-01 0.610718 -4.830 NM_001190718 7.77 12.89 1.60e-06 0.013250 3.928 NM_001013362 7.36 10.04 1.01e-05 0.020405 2.951 NM_008710 7.03 25.52 8.91e-09 0.000248 8.596 NM_001164268 6.96 4.60 1.89e-03 0.214461 -0.887 NM_001136484 6.96 10.54 7.11e-06 0.020405 3.334 [1] 27798 Warning message: Removed 4 rows containing missing values (geom_point). sample condition 1 mN5 mN 2 mN7 mN 3 mP1 mP 4 mP3 mP 5 mP5 mP 6 mT3 mT 7 mT5 mT 8 mT8 mT sample condition 1 mN5 mN 2 mN7 mN 3 mP1 mP 4 mP3 mP 5 mP5 mP 6 mT3 mT 7 mT5 mT 8 mT8 mT path 1 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654626 2 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654628 3 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654633 4 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654636 5 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654637 6 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654639 7 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654641 8 /drone/src/github.com/greenelab/continuous_analysis_rnaseq/kallisto_output/SRR1654643 $ git config user.email "brettbj@gmail.com" $ git config user.name "Brett Beaulieu-Jones" $ git config --global push.default simple $ git remote set-url origin https://github.com/greenelab/continuous_analysis_rnaseq.git $ git checkout master Already on 'master' M kallisto_output/SRR1654626/abundance.h5 M kallisto_output/SRR1654626/run_info.json M kallisto_output/SRR1654628/abundance.h5 M kallisto_output/SRR1654628/run_info.json M kallisto_output/SRR1654633/abundance.h5 M kallisto_output/SRR1654633/run_info.json M kallisto_output/SRR1654636/abundance.h5 M kallisto_output/SRR1654636/run_info.json M kallisto_output/SRR1654637/abundance.h5 M kallisto_output/SRR1654637/run_info.json M kallisto_output/SRR1654639/abundance.h5 M kallisto_output/SRR1654639/run_info.json M kallisto_output/SRR1654641/abundance.h5 M kallisto_output/SRR1654641/run_info.json M results/PCA.png M results/res_mNvsmP.png M results/res_mTvsmN.png $ git add kallisto_output $ git add results $ git commit -a -m "Drone Build [skip ci] [ci skip]" [master 99877f9] Drone Build [skip ci] [ci skip] 20 files changed, 35043 insertions(+), 7 deletions(-) rewrite kallisto_output/SRR1654637/abundance.h5 (61%) create mode 100644 kallisto_output/SRR1654643/abundance.h5 create mode 100644 kallisto_output/SRR1654643/abundance.tsv create mode 100644 kallisto_output/SRR1654643/run_info.json rewrite results/PCA.png (79%) rewrite results/res_mNvsmP.png (88%) rewrite results/res_mTvsmN.png (87%) $ git remote set-url origin https://brettbj:a2a55d6a8160d0677ce92630e8e9ee194889ee34@github.com/greenelab/continuous_analysis_rnaseq.git $ git push --set-upstream origin master To https://brettbj:a2a55d6a8160d0677ce92630e8e9ee194889ee34@github.com/greenelab/continuous_analysis_rnaseq.git e321ad0..99877f9 master -> master Branch master set up to track remote branch master from origin.