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Cellranger error

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
}
10x multiplexing single cell
• 2,485 views • link
updated by GenoMax GenoMax • written by zizigolu zizigolu

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?

• 0 views • link
written by GenoMax GenoMax

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]$

• 0 views • link
written by zizigolu zizigolu

[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.

• 0 views • link
written by GenoMax GenoMax

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?

• 0 views • link
written by zizigolu zizigolu

As CMOs found in gex fastq files and I swapped the names

If the folder structure does not match the configuration in the CSV file then you could get an error since the right files will not be in the right folder. If the file names appear swapped (from your other thread), you should reach out to whoever generated the data and make them aware of the discrepancy. Also make sure there are no other surprises.

• 0 views • link
written by GenoMax GenoMax

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