Hi Biostars Users,
I would like to know if you have encountered this issue while working with CONTRA tool http://sourceforge.net/apps/mediawiki/contra-cnv/index.php?title=CONTRA:_Copy_Number_Analysis_for_Targeted_Resequencing#Examples) for detecting CNVs in targeted NGS.
In fact, my analysis is "stopping" at the binning process with no error message, I have checked all the required arguments and they seem to be ok :
contra.py --target 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam --fasta genome.fa -o /contraresults/re1
target : 0247401_D_BED_20090724_hg19_MERGED.bed
test : P0667T_GATKrealigned_duplicates_marked.bam
control : P0667N_GATKrealigned_duplicates_marked.bam
outfolder : /work/home/shilab/exomedata/UCSU_Homo_sapiens_hg19_testcontra/contraresults/ctc1
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.
Converting TEST Sample...
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam P0667T_GATKrealigned_duplicates_marked.bam -bga -g /work/home/shilab/e
DEBUG 123 genomeCoverageBed -ibam P0667N_GATKrealigned_duplicates_marked.bam -bga -g /work/home/shilab/e
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
Getting targeted regions DOC...
chr1
chr6
chr10
chr11
chr7
chr12
chr8
chr13
chr14
chr15
chr9
chrX
chr16
chr17
Targeted regions pre-processing: Done
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
Targeted regions pre-processing: Done
Test file read depth = 337238927
Control file read depth = 304812391
Pre-processing Completed.
Getting the Log Ratio ...
Binning ...
End of assign.bin.number.py with 11620 exons in 3 bins
Significance Test ...
Process Process-3:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
self._target(self._args, *self._kwargs)
File "/work/home/shilab/exome/CONTRA.v2.0.8/contra.py", line 413, in analysisPerBin
rscr = subprocess.call(args)
File "/usr/lib64/python2.6/subprocess.py", line 478, in call
p = Popen(popenargs, *kwargs)
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
raise child_exception
OSError: [Errno 2] No such file or directory
Temp Folder Removed
Done...
do you know the error ‘OSError: [Errno 2] No such file or directory’ ？ and how to solve the problem？
thank you for your help
Kiz
