Hi all,
I'm starting to use CONTRA to detect loss/gain of exons in my dozen of samples and I got a first issue to generate the baseline..
Here is the error :
python $contra_dir/baseline.py -t annotations/BR_genes_exons_hg19_m20p10.bed -o output -n N2R -f /N2R10/N2R10.onExons.bam /N2R2/N2R2.onExons.bam /N2R11/N2R11.onExons.bam /N2R3/N2R3.onExons.bam /N2R12/N2R12.onExons.bam /N2R4/N2R4.onExons.bam /N2R13/N2R13.onExons.bam /N2R5/N2R5.onExons.bam /N2R14/N2R14.onExons.bam
------ baseline.py -------
Target: /annotations/BRCA_exons_hg19_m20p10.bed
File: /N2R10/N2R10.onExons.bam
File: /N2R2/N2R2.onExons.bam
File: /N2R11/N2R11.onExons.bam
File: /N2R3/N2R3.onExons.bam
File: /N2R12/N2R12.onExons.bam
File: /N2R4/N2R4.onExons.bam
File: /N2R13/N2R13.onExons.bam
File: /N2R5/N2R5.onExons.bam
File: /N2R14/N2R14.onExons.bam
Output Directory: output
----- creating output directory -----
output
output/buf
----- Processing Files -----
output/buf/N2R10.onExons.bam
output/buf/N2R2.onExons.bam
output/buf/N2R11.onExons.bam
output/buf/N2R3.onExons.bam
output/buf/N2R12.onExons.bam
output/buf/N2R4.onExons.bam
output/buf/N2R13.onExons.bam
Traceback (most recent call last):
File "CONTRA.v2.0.2/baseline.py", line 149, in <module>
pool.map(processInFile,infiles)
File "/usr/lib/python2.6/multiprocessing/pool.py", line 148, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.6/multiprocessing/pool.py", line 422, in get
raise self._value
OSError: [Errno 2] No such file or directory
output/buf/N2R5.onExons.bam
Have you any idea what is wrong here?
Thanks for your help.
I'm starting to use CONTRA to detect loss/gain of exons in my dozen of samples and I got a first issue to generate the baseline..
Here is the error :
python $contra_dir/baseline.py -t annotations/BR_genes_exons_hg19_m20p10.bed -o output -n N2R -f /N2R10/N2R10.onExons.bam /N2R2/N2R2.onExons.bam /N2R11/N2R11.onExons.bam /N2R3/N2R3.onExons.bam /N2R12/N2R12.onExons.bam /N2R4/N2R4.onExons.bam /N2R13/N2R13.onExons.bam /N2R5/N2R5.onExons.bam /N2R14/N2R14.onExons.bam
------ baseline.py -------
Target: /annotations/BRCA_exons_hg19_m20p10.bed
File: /N2R10/N2R10.onExons.bam
File: /N2R2/N2R2.onExons.bam
File: /N2R11/N2R11.onExons.bam
File: /N2R3/N2R3.onExons.bam
File: /N2R12/N2R12.onExons.bam
File: /N2R4/N2R4.onExons.bam
File: /N2R13/N2R13.onExons.bam
File: /N2R5/N2R5.onExons.bam
File: /N2R14/N2R14.onExons.bam
Output Directory: output
----- creating output directory -----
output
output/buf
----- Processing Files -----
output/buf/N2R10.onExons.bam
output/buf/N2R2.onExons.bam
output/buf/N2R11.onExons.bam
output/buf/N2R3.onExons.bam
output/buf/N2R12.onExons.bam
output/buf/N2R4.onExons.bam
output/buf/N2R13.onExons.bam
Traceback (most recent call last):
File "CONTRA.v2.0.2/baseline.py", line 149, in <module>
pool.map(processInFile,infiles)
File "/usr/lib/python2.6/multiprocessing/pool.py", line 148, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.6/multiprocessing/pool.py", line 422, in get
raise self._value
OSError: [Errno 2] No such file or directory
output/buf/N2R5.onExons.bam
Have you any idea what is wrong here?
Thanks for your help.
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