MERLoT
Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpAzFAbr/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
bash: bin/activate: No such file or directory
Loaded Tree Topology Library...
Data Dimensions (92, 1)
Calculating distances...
Calculating Scaffold Tree...
[Note: EndPoints search terminated because no further positive scores were found...]
Only 2 Endpoints detected.
Endpoints: 2 14 68
Branchpoints: 0 0
Tree_Branch: 13 67
Endpoints: 2 13 67
Finished Scaffold Tree... 0.18648076057434082 seconds
Error in 1:dim(ScaffoldTree$Branches)[1] : argument of length 0
Calls:
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpg2qaD5/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
bash: bin/activate: No such file or directory
Loaded Tree Topology Library...
Traceback (most recent call last):
File "/usr/local/lib/R/site-library/merlot/python/ScaffoldTree.py", line 286, in
Coordinates = pd.read_csv(DMCoordinates, sep = "\t", header=None)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 646, in parser_f
return _read(filepath_or_buffer, kwds)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 389, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 730, in __init__
self._make_engine(self.engine)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 923, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 1390, in __init__
self._reader = _parser.TextReader(src, **kwds)
File "pandas/parser.pyx", line 538, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:6171)
pandas.io.common.EmptyDataError: No columns to parse from file
Error in file(file, "rt") : cannot open the connection
Calls: -> read_topology -> -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/tmp/RtmpcBUVHB/file6d83ef67bfe_TreeTopology.dat': No such file or directory
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpjd3nV2/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
bash: bin/activate: No such file or directory
Loaded Tree Topology Library...
Traceback (most recent call last):
File "/usr/local/lib/R/site-library/merlot/python/ScaffoldTree.py", line 286, in
Coordinates = pd.read_csv(DMCoordinates, sep = "\t", header=None)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 646, in parser_f
return _read(filepath_or_buffer, kwds)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 389, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 730, in __init__
self._make_engine(self.engine)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 923, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/usr/lib/python3/dist-packages/pandas/io/parsers.py", line 1390, in __init__
self._reader = _parser.TextReader(src, **kwds)
File "pandas/parser.pyx", line 538, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:6171)
pandas.io.common.EmptyDataError: No columns to parse from file
Error in file(file, "rt") : cannot open the connection
Calls: -> read_topology -> -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/tmp/Rtmpw3WTar/filec08a233ab7c9_TreeTopology.dat': No such file or directory
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpj3yWCt/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
bash: bin/activate: No such file or directory
Loaded Tree Topology Library...
Data Dimensions (355, 1)
Calculating distances...
Calculating Scaffold Tree...
Only 2 Endpoints detected.
Endpoints: 2 107 209
Branchpoints: 0 0
Tree_Branch: 106 208
Endpoints: 2 106 208
Finished Scaffold Tree... 3.702293634414673 seconds
Error in 1:dim(ScaffoldTree$Branches)[1] : argument of length 0
Calls:
Execution halted
File: /home/rcannood/Workspace/dynverse/dynbenchmark//derived/04-method_characterisation/method_testing/suite/merlot/r2gridengine/20180803_183346_merlot_IJUEieqC6s/log/log.5.e.txt
Part of 