write_clusters_from_nc_folders exit with error on SLURM but ran successfully on command line

[WeimingWHu]

For the avamb workflow, "write_clusters_from_nc_folders" exit with error when running as a SLURM job. the error messages as follow:
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
I could not track down what is the problem, as the "final_avamb_clusters_written.log" file is empty.
But when I ran this on interactive session, it finished without error.
Maybe there is a minor bug somewhere in the script "write_clusters_from_dereplicated_and_ripped_bins.sh", it did not produce avamb_manual_drep_disjoint_clusters.tsv and the next step that remove all the tmp files around.

[Paupiera]

Hi,

Apologies for the late reply. It is not the first time we have encountered issues while executing bash scripts. I have replaced the bash script with a Python script, it would be great if you could give it a try since we do not use SLURM in our machines. Please let me know how it goes with the new script.

Best,