CONTRA for exon CNV detection. troubleshooting'no such file or director'
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5.0 years ago

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

CNV exon NGS contra • 1.6k views
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