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MikkelSchubert avatar MikkelSchubert commented on July 29, 2024

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

from paleomix.

renhamm avatar renhamm commented on July 29, 2024

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

from paleomix.

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