Error in CONTRA
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Entering edit mode
5.9 years ago
Folder40g ▴ 170

Hi.

I'm using CONTRA and I get back the next error which I have not been able to solve. I'm missing something. Thanks for your time.

python /home/Programas/CONTRA.v2.0.6/contra.py -t /local/CLL/WES_libraries/S04380219_V5/V5_covered_noHead.bed -s /local/CLL/Processing/FGO/Alignment/FGO_20120918_PERIPHERALBLOOD_f4_RG_Reordered_deduplicated_Realigned_BCalibrated.bam -c /local/CLL/Processing/FGO/Alignment/FGO_NORMAL_E1_f4_RG_Reordered_deduplicated_Realigned_BCalibrated_NORMAL.bam -f /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.7.10-r789/genome.fa --sampleName=FGO_20120918_PERIPHERALBLOOD -o /local/CLL/CNV/FGO/Peripheralblood
target      : /local/CLL/WES_libraries/S04380219_V5/V5_covered_noHead.bed
test        : /local/CLL/Processing/FGO/Alignment/FGO_20120918_PERIPHERALBLOOD_f4_RG_Reordered_deduplicated_Realigned_BCalibrated.bam
control     : /local/CLL/Processing/FGO/Alignment/FGO_NORMAL_E1_f4_RG_Reordered_deduplicated_Realigned_BCalibrated_NORMAL.bam
fasta       : /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.7.10-r789/genome.fa
outfolder   : /local/CLL/CNV/FGO/Peripheralblood
numBin      : [20]
minreaddepth    : 10
minNBases   : 10
sam     : False
pval        : 0.05
sampleName  : FGO_20120918_PERIPHERALBLOOD
nomultimapped   : False
plot        : False
bedInput        : False
minExon     : 2000
largeDeletion   : False
removeDups  : False
Creating Output Folder :  Done.
Traceback (most recent call last):
  File "/home/Programas/CONTRA.v2.0.6/contra.py", line 613, in <module>
    main()
  File "/home/Programas/CONTRA.v2.0.6/contra.py", line 558, in main
    get_genome(params.TEST, genomeFile)
  File "/home/Programas/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 "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Just in case I did try with python 2.6.9 instead of 2.7.6 and it's not working either.

CONTRA • 1.6k views
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Just a silly check. Are the files present in the given paths? Because the program is complaining about a missing file...

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Yes, files path seem to be written correctly.

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It seems an error of the python modules that belong to this program. It is not error of the path of the input files. Check the dependencies of the python and the R modules in the code. Is bedtools properly installed? Did you do the installation of the bedtools module properly while installing contra? Another this is check if you genome file and the bam files have indexes or not, you need to crea genome.fa.fai and for the bam their corresponding *.bam.bai files. This is what I can understand while taking a look at the python code

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