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Old 08-14-2015, 12:58 PM   #1
DNAmethylome
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Location: usa

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Default CONTRA error messages (need urgent help!)

Hi,

I am using the tool CONTRA, and getting some error messages as below:
---------
Process Process-1:
Process Process-2:
Traceback (most recent call last):
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
self._target(*self._args, **self._kwargs)
self._target(*self._args, **self._kwargs)
File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 371, in convertBam
File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 371, in convertBam
output = subprocess.Popen(args, stdout = iOutFile).wait()
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
output = subprocess.Popen(args, stdout = iOutFile).wait()
raise child_exception
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
OSError: [Errno 2] No such file or directory
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 613, in <module>
main()
File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 583, in main
t1 = int(file.readlines(open(folder+"temp.txt"))[0].strip("\n"))
IOError: [Errno 2] No such file or directory: '/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt'

---------------------------------

Does this seem a python process/subprocess issue? I have also downloaded python version 2.7, but I have got the same error messages.


Thanks,

-J
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Old 08-20-2015, 07:05 AM   #2
DNAmethylome
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Default

Can anyone help on this?
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Old 08-20-2015, 12:19 PM   #3
GenoMax
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Are you using this with a job scheduler/on a cluster? Is this (/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt) path available on execution node, if it is the latter.
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Old 08-21-2015, 05:56 AM   #4
Zaag
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Did you reinstall before trying with python2.7?
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Old 08-21-2015, 07:20 AM   #5
DNAmethylome
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Quote:
Originally Posted by GenoMax View Post
Are you using this with a job scheduler/on a cluster? Is this (/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt) path available on execution node, if it is the latter.
Hi,thanks for the reply.
I was running this on a cluster (using condor). So, this is the path/file that CONTRA would generate during the run. It seems to me that, because of some issues with either the contra script or with python, that this file was not successfully generated. That's why I got such message, and I am trying to figure out why exactly this file was not generated..
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Old 08-21-2015, 07:59 AM   #6
DNAmethylome
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Quote:
Originally Posted by Zaag View Post
Did you reinstall before trying with python2.7?
Hi, thanks for the input.

I am currently using python 2.6.6.
Someone was suggesting these error messages were due to python version issue, and after they switched to python 2.7, the issues were fixed. However, I have tried python 2.7, and I just got the same error messages.......

Thanks,
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Old 08-22-2015, 03:31 AM   #7
Zaag
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Quote:
Originally Posted by DNAmethylome View Post
Hi, thanks for the input.

I am currently using python 2.6.6.
Someone was suggesting these error messages were due to python version issue, and after they switched to python 2.7, the issues were fixed. However, I have tried python 2.7, and I just got the same error messages.......

Thanks,
Sorry if you already understood but you need to install contra again with python2.7 for it to work.
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Old 08-23-2015, 08:19 AM   #8
DNAmethylome
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Quote:
Originally Posted by Zaag View Post
Sorry if you already understood but you need to install contra again with python2.7 for it to work.
Hi Zaag, thanks for the input. As you suggested, I just re-installed python2.7.10, and ran contra with python 2.7.10, and I still got similar error messages.

Command line:
--------------------------------------
/home/files/test/bin/Python-2.7.10/python /home/files/test/bin/CONTRA.v2.0.6/contra.py --target /home/files/test/test/scripts/Panels/project/ref_files/panel_target_latest1.bed --test /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_TD/calls/ok.bam --control /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/ok.bam --fasta /usr/local/mrgstorage/refseq/build.hg19.GRCh37.p13/hg19_GRCh37_p13_full.fasta --outFolder /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/contra1
----------------------------------------

Log/Error
----------------------------------------
target : /home/files/test/test/scripts/Panels/project/ref_files/panel_target_latest1.bed
test : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_TD/calls/ok.bam
control : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/ok.bam
fasta : /usr/local/mrgstorage/refseq/build.hg19.GRCh37.p13/hg19_GRCh37_p13_full.fasta
outfolder : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/contra1
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
Traceback (most recent call last):
File "/home/files/test/bin/CONTRA.v2.0.6/contra.py", line 613, in <module>
main()
File "/home/files/test/bin/CONTRA.v2.0.6/contra.py", line 558, in main
get_genome(params.TEST, genomeFile)
File "/home/files/test/bin/CONTRA.v2.0.6/scripts/get_chr_length.py", line 31, in get_genome
raw_header = subprocess.Popen(args, stdout = subprocess.PIPE).communicate()[0]
File "/home/files/test/bin/Python-2.7.10/Lib/subprocess.py", line 710, in __init__
errread, errwrite)
File "/home/files/test/bin/Python-2.7.10/Lib/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
----------------------------------------


Do you think I was missing something here?...

Thanks!

-J
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