Cellranger error

Question

[zizigolu]

Hi

Please, anybody knows what this error is in cellranger

2025-11-21 18:01:31 [runtime] (failed)          ID.multi_HB216_GRCh38.SC_MULTI_CS.SC_MULTI_CORE.SAMPLE_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork_HB216_T1

[error] Pipestance failed. Error log at:
multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uc55520a8d9/_errors

Log message:
Traceback (most recent call last):
  File "/parallel_scratch/fi0001/cellranger/external/martian/adapters/python/martian_shell.py", line 648, in _main
    stage.main()
  File "/parallel_scratch/fi0001/cellranger/external/martian/adapters/python/martian_shell.py", line 617, in main
    self._run(
  File "/parallel_scratch/fi0001/cellranger/external/martian/adapters/python/martian_shell.py", line 564, in _run
    cmd()
  File "/parallel_scratch/fi0001/cellranger/external/martian/adapters/python/martian_shell.py", line 618, in <lambda>
    lambda: self._module.join(args, outs, chunk_defs, chunk_outs)
  File "/parallel_scratch/fi0001/cellranger/mro/rna/stages/analyzer/summarize_analysis/__init__.py", line 92, in join
    cr_io.hardlink_with_fallback(chunk_out.analysis, outs.analysis)
  File "/parallel_scratch/fi0001/cellranger/lib/python/cellranger/cr_io.py", line 191, in hardlink_with_fallback
    shutil.copytree(src, dst, copy_function=_hardlink_file_with_fallback, dirs_exist_ok=True)
  File "/parallel_scratch/fi0001/cellranger/external/anaconda/lib/python3.10/shutil.py", line 558, in copytree
    return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
  File "/parallel_scratch/fi0001/cellranger/external/anaconda/lib/python3.10/shutil.py", line 512, in _copytree
    raise Error(errors)
shutil.Error: [('/users/fi0001/scratch/bin/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/chnk0-uc55520a8de/files/analysis/analysis.h5', '/users/fi0001/scratch/bin/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uc55520a8d9/files/analysis/analysis.h5', "[Errno 11] Resource temporarily unavailable: '/users/fi0001/scratch/bin/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/chnk0-uc55520a8de/files/analysis/analysis.h5' -> '/users/fi0001/scratch/bin/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uc55520a8d9/files/analysis/analysis.h5'")]


2025-11-21 18:01:31 Shutting down.
2025-11-21 18:01:31 [jobmngr] Highest memory usage observed: {
  "rss": 16764272640,
  "shared": 228569088,
  "vmem": 19005997056,
  "text": 104480768,
  "stack": 17057574912,
  "proc_count": 55
}

[GenoMax]

What does this file contain multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uc55520a8d9/_errors?

[zizigolu]

Thank you, says

[fi0001@login1 (eureka2) hb216_cleanrun]$ cat multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZ
ER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uf30221af8d/_errors
Traceback (most recent call last):
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/martian/adapters/python/martian_shell.py", line 648, in _main
    stage.main()
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/martian/adapters/python/martian_shell.py", line 617, in main
    self._run(
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/martian/adapters/python/martian_shell.py", line 564, in _run
    cmd()
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/martian/adapters/python/martian_shell.py", line 618, in <lambda>
    lambda: self._module.join(args, outs, chunk_defs, chunk_outs)
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/mro/rna/stages/analyzer/summarize_analysis/__init__.py", line 92, in join
    cr_io.hardlink_with_fallback(chunk_out.analysis, outs.analysis)
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/lib/python/cellranger/cr_io.py", line 191, in hardlink_with_fallback
    shutil.copytree(src, dst, copy_function=_hardlink_file_with_fallback, dirs_exist_ok=True)
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/anaconda/lib/python3.10/shutil.py", line 558, in copytree
    return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
  File "/parallel_scratch/fi0001/cellranger1/cellranger-9.0.1/external/anaconda/lib/python3.10/shutil.py", line 512, in _copytree
    raise Error(errors)
shutil.Error: [('/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/chnk0-uf30221af8f/files/analysis/analysis.h5', '/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uf30221af8d/files/analysis/analysis.h5', "[Errno 11] Resource temporarily unavailable: '/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/chnk0-uf30221af8f/files/analysis/analysis.h5' -> '/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uf30221af8d/files/analysis/analysis.h5'")]
[fi0001@login1 (eureka2) hb216

_cleanrun]$

[GenoMax]

[Errno 11] Resource temporarily unavailable: '/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/chnk0-uf30221af8f/files/analysis/analysis.h5' -> '/users/fi0001/scratch/hb216_cleanrun/multi_HB216_GRCh38/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_HB216_T1/join-uf30221af8d/files/analysis/analysis.h5'")]

Looks like there may have been a glitch on the storage file system.

Try the run again and see if it completes this time.

If it errors out on the same file then you may have a corrupt file/dataset.

[zizigolu]

As CMOs found in gex fastq files and I swapped the names (I put gex fastq files for multiplex data and vise versa), could this make this error?