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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Cellranger count error version3.1.0 #90

Closed martitroiani closed 3 years ago

martitroiani commented 4 years ago

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

evolvedmicrobe commented 3 years ago

Hi, I'd recommend using the latest version of cellranger. Please contact support@10xgenomics.com for further help with this issue.