search

10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
Other
366 stars 94 forks source link

Cellranger-arc peak annotation error - bedtools #224

Closed yigitbabal closed 1 year ago

yigitbabal commented 1 year ago

Hello,

I am trying to run cellranger-arc count by custom reference genome. cellranger-arc mkref worked very well. However I am getting an error during cellranger-arc count during peak annotation. How can I solve this error, do you know anything about that?

Best regards, Yigit

Error log:

2023-08-18 00:59:21 [runtime] (failed) ID.acomys.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS

[error] Pipestance failed. Error log at: acomys/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02-u04c6dea638/_errors

Log message: Traceback (most recent call last): File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 659, in _main stage.main() File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in main self._run(lambda: self._module.main(args, outs)) File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 589, in _run cmd() File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in self._run(lambda: self._module.main(args, outs)) File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/mro/atac/stages/analysis/annotate_peaks/init.py", line 73, in main annotations = annotate_peaks(peak_chunk, args.reference_path) File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/lib/python/atac/analysis/annotation.py", line 198, in annotate_peaks transcripts_filtered, wa=True, wb=True File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/site-packages/pybedtools/bedtool.py", line 917, in decorated result = method(self, *args, **kwargs) File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/site-packages/pybedtools/bedtool.py", line 401, in wrapped decode_output=decode_output, File "/crex/proj/spatialals/workspace/ykbabal/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/site-packages/pybedtools/helpers.py", line 460, in call_bedtools raise BEDToolsError(subprocess.list2cmdline(cmds), stderr) pybedtools.helpers.BEDToolsError: Command was:

bedtools intersect -wb -wa -b /proj/spatialals/Acomys/multiome_updated/acomys/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02-u04c6dea638/tmp/pybedtools.9_m9igl3.tmp -a /proj/spatialals/Acomys/multiome_updated/acomys/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02-u04c6dea638/tmp/pybedtools.emea0no1.tmp

Error message was: Error: line number 548 of file /proj/spatialals/Acomys/multiome_updated/acomys/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02-u04c6dea638/tmp/pybedtools.emea0no1.tmp has 4 fields, but 5 were expected.

evolvedmicrobe commented 1 year ago

Please send this issue to support@10xgenomics.com and someone will follow up with you.