Hi,
I'm aligning 10x cell data with cellranger count but I'm having problems in the alignment step.
This is the error
Log message:
Traceback
(most recent call last):
File
"path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py",
line 589, in _main
stage.main()
File
"path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py",
line 554, in main
self._run(lambda: self._module.main(args,
outs))
File
"path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py",
line 523, in _run
cmd()
File "path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py",
line 554, in
self._run(lambda: self._module.main(args,
outs))
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/init.py",
line 128, in main
align_reads(args, outs)
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/init.py",
line 67, in align_reads
read_group_tags=tk_bam.make_star_rg_header(args.read_group))
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/reference.py",
line 616, in align
raise cr_io.CRCalledProcessError(e.msg + '
Check STAR logs for errors: %s .' % star_log)
CRCalledProcessError:
Process returned error code -7: STAR . Check STAR logs for errors:
Can someone help me because I don't know how to solve the problem.
Thank you in advance
Best
Hi, I'm aligning 10x cell data with cellranger count but I'm having problems in the alignment step. This is the error
Log message: Traceback (most recent call last): File "path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 589, in _main stage.main() File "path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in main self._run(lambda: self._module.main(args, outs)) File "path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 523, in _run cmd() File "path/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in
self._run(lambda: self._module.main(args,
outs))
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/init.py",
line 128, in main
align_reads(args, outs)
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/init.py",
line 67, in align_reads
read_group_tags=tk_bam.make_star_rg_header(args.read_group))
File
"path/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/reference.py",
line 616, in align
raise cr_io.CRCalledProcessError(e.msg + '
Check STAR logs for errors: %s .' % star_log)
CRCalledProcessError:
Process returned error code -7: STAR . Check STAR logs for errors:
Can someone help me because I don't know how to solve the problem. Thank you in advance Best