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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
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Errors running node #51

Closed renhamm closed 1 year ago

renhamm commented 1 year ago

When running the bam pipeline, I quickly hit a confusing error (see below). I have tried running this script on every available partition, with variable memory and CPU allocations, but the error remains the same. How do I fix this?

15:34:04 INFO [1/270] Started trimming PE adapters from '/global/scratch/users/l aurenhamm/thesis/aim1/Alignment_v3/fastq_original/1_5_S12ID[12].fastq' 15:34:04 ERROR NodeError while trimming PE adapters from '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/1_5_S12ID[12].fastq': 15:34:04 INFO Saving error logs to '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/paleomix/bamOuts/bam_pipeline.20230717_153402_01.log' 15:34:04 ERROR Error(s) running Node: 15:34:04 ERROR Temporary directory: '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca' 15:34:04 ERROR 15:34:04 ERROR Command = AdapterRemoval --gzip --trimns --trimqualities --threads 12 --basename \ 15:34:04 ERROR /global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca/reads \ 15:34:04 ERROR --collapse --file1 \ 15:34:04 ERROR /global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/1_5_S12_ID_1.fastq \ 15:34:04 ERROR --file2 \ 15:34:04 ERROR /global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/1_5_S12_ID_2.fastq \ 15:34:04 ERROR --mm 3 --minlength 25 --qualitybase 33 --qualitybase-output 33 15:34:04 ERROR Status = Exited with return-code 1 15:34:04 ERROR STDOUT = '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca/pipe_AdapterRemoval_47368337539856.stdout' 15:34:04 ERROR STDERR = '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca/pipe_AdapterRemoval_47368337539856.stderr' 15:34:04 ERROR CWD = '/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/paleomix/bamOuts'

MikkelSchubert commented 1 year ago

You'll need to check the actual output from the command that failed to figure out what went wrong.

For AdapterRemoval you'll most likely you'll be able to figure out what the problem is from that based on the error messages printed to STDERR and written to the STDERR file. Based on the log messages you copy/pasted, the file is

/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca/pipe_AdapterRemoval_47368337539856.stderr

But for other programs (or if the STDERR file doesn't provide enough information) you should also check the STDOUT file, e.g:

/global/scratch/users/laurenhamm/thesis/aim1/Alignment_v3/fastq_original/5d71e6f0-32c6-41cc-b1f3-bbd9efca5eca/pipe_AdapterRemoval_47368337539856.stdout

Best, Mikkel

renhamm commented 1 year ago

Thanks! I was looking at the SLURM output file on accident! You can close this thread.