There are at least two things going on here. One of the errors seems
to come from your scheduler(?):
"""
/cm/local/apps/sge/var/spool/usnee1-lph001-n062/job_scripts/6960547: line
156: moduel: command not found
"""
The other messages indicate that one of the last steps in the LoFreq
Somatic analysis failed. Key message is:
"""
CRITICAL [2014-08-23 20:34:46,702]: The following command failed: lofreq
uniq --uni-freq 0.5 --uniq-mtc fdr --uniq-alpha 0.001 -v
"""
Unfortunately it doesn't tell you why it failed. Did you by any chance
call the program in verbose mode and could check the log file? If not,
could you simply delete the file called
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_final.vcf'
and rerun 'lofreq somatic' with added options '-v --continue'? This
will reuse existing files and try to complete the analysis in verbose
mode. Alternatively, run the 'lofreq uniq' step manually with added
'--verbose' (after deleting the aforementioned files). This will
likely fail again but at least tell you what's going on.
Hi,
While running LoFreq, I've got the following error.
/cm/local/apps/sge/var/spool/usnee1-lph001-n062/job_scripts/6960547: line
156: moduel: command not found
CRITICAL [2014-08-23 20:34:46,702]: The following command failed: lofreq
uniq --uni-freq 0.5 --uniq-mtc fdr --uniq-alpha 0.001 -v
/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_raw.vcf.gz
-o
/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_final.vcf
/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/bam/CNTR5_NORMAL/NORMAL.final.bam
(Command '['lofreq', 'uniq', '--uni-freq', '0.5', '--uniq-mtc', 'fdr',
'--uniq-alpha', '0.001', '-v',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_raw.vcf.gz',
'-o',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_final.vcf',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/bam/CNTR5_NORMAL/NORMAL.final.bam']'
returned non-zero exit status 1)
CRITICAL [2014-08-23 20:34:46,702]: An error message indicating the source
of this error should have bee printed above
CRITICAL [2014-08-23 20:34:46,702]: Somatic SNV caller failed. Exiting
Traceback (most recent call last):
File
"/site/ne/home/wings/bfx_tools/lofreq/v2.0.0/bin/lofreq2_somatic.py", line
663, in <module>*
main()*
File
"/site/ne/home/wings/bfx_tools/lofreq/v2.0.0/bin/lofreq2_somatic.py", line
655, in main*
somatic_snv_caller.run()*
File
"/site/ne/home/wings/bfx_tools/lofreq/v2.0.0/bin/lofreq2_somatic.py", line
467, in run*
self.uniq()*
File
"/site/ne/home/wings/bfx_tools/lofreq/v2.0.0/bin/lofreq2_somatic.py", line
413, in uniq*
(o, e) = self.subprocess_wrapper(cmd, close_tmp=False)*
File
"/site/ne/home/wings/bfx_tools/lofreq/v2.0.0/bin/lofreq2_somatic.py", line
182, in subprocess_wrapper*
subprocess.check_call(cmd, stdout=fh_stdout, stderr=fh_stderr)*
File
"/site/ne/home/wings/bfx_tools/python/v2.7.6/lib/python2.7/subprocess.py",
line 540, in check_call*
raise CalledProcessError(retcode, cmd)*
subprocess.CalledProcessError: Command '['lofreq', 'uniq', '--uni-freq',
'0.5', '--uniq-mtc', 'fdr', '--uniq-alpha', '0.001', '-v',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_raw.vcf.gz',
'-o',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_final.vcf',
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/bam/CNTR5_NORMAL/NORMAL.final.bam']'
returned non-zero exit status 1
Do you have any insights on this? Thanks.
Best,
Joon
Hi Joon
There are at least two things going on here. One of the errors seems
to come from your scheduler(?):
"""
/cm/local/apps/sge/var/spool/usnee1-lph001-n062/job_scripts/6960547: line
156: moduel: command not found
"""
The other messages indicate that one of the last steps in the LoFreq
Somatic analysis failed. Key message is:
"""
CRITICAL [2014-08-23 20:34:46,702]: The following command failed: lofreq
uniq --uni-freq 0.5 --uniq-mtc fdr --uniq-alpha 0.001 -v
"""
Unfortunately it doesn't tell you why it failed. Did you by any chance
call the program in verbose mode and could check the log file? If not,
could you simply delete the file called
'/site/ne/data/bh-results/Wings/AdHoc_Analysis/Target-Seq/Program_SERD/Project_IDT_TEST/LibraryType_IDT_MDM2_SERD/variants/CNTR5_NORMAL/CNTR5.all.lofreq.somatic_final.vcf'
and rerun 'lofreq somatic' with added options '-v --continue'? This
will reuse existing files and try to complete the analysis in verbose
mode. Alternatively, run the 'lofreq uniq' step manually with added
'--verbose' (after deleting the aforementioned files). This will
likely fail again but at least tell you what's going on.
Andreas
On 24 August 2014 09:59, Joon joonlee3@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Thank, Andreas. I will try again with the suggested argument.
Joon