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Old 03-11-2016, 08:18 AM   #33
oxydeepu
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Location: bangalore,india

Join Date: Jul 2011
Posts: 41
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Dear Eric,

Thank you for sparing your time. I tried the target and it gives a 4 field bed. But I gues the problem is coming when I use the BAM files.

###################

cnvkit.py batch /home/deepak/MM02-N_MM02-020200/colossus_analysis/BAM/MM02-020200_MarkDup.bam --normal /home/deepak/MM02-N_MM02-020200/colossus_analysis/BAM/MM02-N_MarkDup.bam --targets Agilent_b37_exome_covered.bed --split --annotate refFlatMod.txt --fasta /home/deepak/Ref/human_g1k_v37_decoy.fasta --access /home/deepak/src/cnvkit/data/access-5k-mappable.hg19.bed --output-reference my_reference.cnn --output-dir results/ --diagram --scatter

Processing reads in MM02-N_MarkDup.bam
Traceback (most recent call last):
File "/usr/local/bin/cnvkit.py", line 4, in <module>
__import__('pkg_resources').run_script('CNVkit==0.7.9.dev0', 'cnvkit.py')
File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 726, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1491, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python2.7/dist-packages/CNVkit-0.7.9.dev0-py2.7.egg/EGG-INFO/scripts/cnvkit.py", line 11, in <module>

File "build/bdist.linux-x86_64/egg/cnvlib/commands.py", line 97, in _cmd_batch

File "build/bdist.linux-x86_64/egg/cnvlib/commands.py", line 172, in batch_make_reference

File "build/bdist.linux-x86_64/egg/cnvlib/parallel.py", line 14, in apply_async
File "build/bdist.linux-x86_64/egg/cnvlib/commands.py", line 193, in batch_write_coverage

File "build/bdist.linux-x86_64/egg/cnvlib/commands.py", line 457, in do_coverage

File "build/bdist.linux-x86_64/egg/cnvlib/coverage.py", line 37, in interval_coverages
File "build/bdist.linux-x86_64/egg/cnvlib/coverage.py", line 110, in interval_coverages_pileup
File "build/bdist.linux-x86_64/egg/cnvlib/coverage.py", line 143, in bedcov
RuntimeError: Bad line from bedcov:
1

#######################

But it does create two bed files.

$ head results/Agilent_b37_exome_covered.*

==> results/Agilent_b37_exome_covered.antitarget.bed <==
chr1 10500 93708 Background
chr1 93708 176917 Background
chr1 227917 267219 Background
chr1 318219 394543 Background
chr1 394543 470868 Background
chr1 521868 563949 Background
chr1 570871 671469 Background
chr1 671469 772067 Background
chr1 772067 872665 Background
chr1 872665 973263 Background

==> results/Agilent_b37_exome_covered.target.bed <==
1 65509 65625 -
1 65831 65973 -
1 69481 69600 OR4F5
1 721381 721519 -
1 721530 721806 -
1 721851 721942 -
1 752916 753035 FAM87B
1 762095 762275 LINC00115
1 762280 762414 LINC00115
1 762420 762565 LINC00115

I have no idea where it is going wrong.

Sorry for a messy and long mail.

Thank you.

Best,
Deepak
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