Closed lineroager closed 1 year ago
Both errors are related in that the software, e.g. conda is no longer found when submitted to the cluster.
But strange why this happens specifically for these rules.
Could you try to simply update to atlas v2.15.2 ?
Yes, this is what I suspected too. It seems the software (Conda, atlas) that I load with my script is not loaded with the next jobs submitted by atlas maybe? I have very limited rights for software installation on the cluster if that would impact something like this.
I will try to update to atlas 2.15.2 and see if it helps. Will be back then!
Edit: Oh, also I think it is happening for these rules specifically because I ran part of the qc locally before moving onto the cluster so these are probably the next rules in the pipeline from where the local execution stopped. Sorry for not mentioning earlier, I kind of forgot I did this.
There is also a anakemake argument that you can supply to the atlas command. it is intended for internal use but It might fix your problem.
--conda-base-path abs path of conda base installation (home of conda, mamba, activate)
I updated to atlas 2.15.2 with no improvement and also tried adding the --conda-base-path to no avail.
In the end I managed to get it running in single machine execution mode, which is not ideal, but works. No conda environments or software is being transferred once atlas submits a new job to the queue, but I did not manage to find a way to fix it.
Going to close this issue since I found a workaround, but feel free to reopen with real solutions any time.
Hello there,
I have been successfully setting up atlas on a Torque cluster, but ran into this error while trying to run qc on a single sample:
The error log of get_read_stats looks like this:
The error log for run_decontamination looks like this:
The cluster log is empty.
I am using atlas version 2.15.1
I saw this issue which had errors in the same rules, but did not mention any solutions before the issue being solved.
I hope you can help, since I am quite stuck and was excited to use atlas on my samples!
Best regards,