Cellranger count fails at chunks_read stage

Question

[dtran822]

I'm running cellranger count for the feature barcode/antibody capture. I keep getting an error during the chunks_read stage. Any help is greatly appreciated.

ID.ty_uv_fb_ear.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS.fork0.join
2022-05-02 11:28:08 [runtime] (failed)          ID.ty_uv_fb_ear.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS

[error] Pipestance failed. Error log at:
ty_uv_fb_ear/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/chnk0-u40246ff887/_errors

Log message:
Traceback (most recent call last):
  File "/lila/data/huse/diana/cellranger-6.1.2/external/martian/adapters/python/martian_shell.py", line 662, in _main
    stage.main()
  File "/lila/data/huse/diana/cellranger-6.1.2/external/martian/adapters/python/martian_shell.py", line 621, in main
    self._run(lambda: self._module.main(args, outs))
  File "/lila/data/huse/diana/cellranger-6.1.2/external/martian/adapters/python/martian_shell.py", line 592, in _run
    cmd()
  File "/lila/data/huse/diana/cellranger-6.1.2/external/martian/adapters/python/martian_shell.py", line 621, in <lambda>
    self._run(lambda: self._module.main(args, outs))
  File "/lila/data/huse/diana/cellranger-6.1.2/mro/rna/stages/feature/summarize_antibody_analysis/__init__.py", line 34, in main
    cr_io.copy(file_path, os.path.join(outs.antibody_analysis, file_name))
  File "/lila/data/huse/diana/cellranger-6.1.2/lib/python/cellranger/io.py", line 165, in copy
    run_command_safely("cp", [src, dst])
  File "/lila/data/huse/diana/cellranger-6.1.2/lib/python/cellranger/io.py", line 102, in run_command_safely
    p = tk_subproc.Popen([cmd] + args, stderr=subprocess.PIPE)
  File "/lila/data/huse/diana/cellranger-6.1.2/lib/python/tenkit/log_subprocess.py", line 98, in Popen
    return subprocess.Popen(args, *wargs, **kwargs)  # pylint: disable=consider-using-with
  File "/lila/data/huse/diana/cellranger-6.1.2/external/anaconda/lib/python3.8/subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/lila/data/huse/diana/cellranger-6.1.2/external/anaconda/lib/python3.8/subprocess.py", line 1702, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'cp': 'cp'

[swbarnes2]

You should probably contact 10XGenomics support.