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Error when executing centrifuge "Argument list too long" #258
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What was your running command for Centrifuge? |
I am using snakemake (7.26) to run the command in the following rule,
This translates into,
My centrifugeSampleSheet.tsv file looks like this (I haven't had any issues with these in prior smaller batches):
In my workflow I have steps prior to this which aggregate a larger number of files into asingle command line parameter for input and did not have this error (seqkit stats). Here is the module which loads snakemake on the HPC I am using,
|
Update. I have been able to repeat the error. launching the workflow via a small sbatch script, as before.
The error message appears,
However, when I run the snakemake centrifugeGTDB rule interactively on the CLI (as below) I do not get the error message, and centrifuge appears to be running correctly.
It is unclear where this behavior is arising from, but my suspicion is that -- because centrifuge runs without error when launched interactively via snakemake -- it is not related to centrifuge. |
The error seems to still be happening, even when launched interactively. It just takes longer to happen, could it be happening after the index loads?
From the logs,
Job ID - 36082140
I will try to batch the job into smaller groups on Monday to see if the error persists. |
Hi,
I am executing centrifuge in batch mode using snakemake on a slurm cluster, and am getting the following error message:
Can't exec "/home/perrybe/.conda/envs/centrifuge/bin/centrifuge-class": Argument list too long at /home/perrybe/.conda/envs/centrifuge/bin/centrifuge line 695. (ERR): Could not open Centrifuge pipe: '/home/perrybe/.conda/envs/centrifuge/bin/centrifuge-class --wrapper basic-0 -x /nesi/nobackup/agresearch03843/centrifuge/centrifuge/GTDB -t --threads 32 - -separator --passthrough -U results/02_kneaddata/FID274912.fastq, [...]
I have 9632 samples I am attempting to run in the batch, in the format
results/02_kneaddata/FID274912.fastq
.I am using a dedicated conda environment to execute in:
The unix system has the following configuration,
I've seen xargs mentioned in other issues with an
"Argument list too long"
error; however, to my reading none of them addressed this issue.Thank you for your time,
Ben
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