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rhysnewell / aviary

A hybrid assembly and MAG recovery pipeline (and more!)
GNU General Public License v3.0
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CheckM Rosella file not found #194

Open sternp opened 10 months ago

sternp commented 10 months ago

Hey Rhys,

There seems to be an issue with the rule checkm_rosella for which it'd be great to get your insight on.

The initial error message is:

Error in rule checkm_rosella:
    jobid: 23
    input: data/rosella_bins/done
    output: data/rosella_bins/checkm2_out, data/rosella_bins/checkm.out
    log: logs/checkm_rosella.log (check log file(s) for error details)
    conda-env: /mnt/hpccs01/work/microbiome/conda/11e1a371ef3335e629225ddf170c50f3_

RuleException:
CalledProcessError in file /mnt/hpccs01/work/microbiome/sw/aviary_repos/aviary-v0.8.3/aviary/aviary/modules/binning/binning.smk, line 419:
Command 'source /mnt/hpccs01/work/microbiome/conda/envs/aviary-v0.8.3/bin/activate '/mnt/hpccs01/work/microbiome/conda/11e1a371ef3335e629225ddf170c50f3_'; set -euo pipefail;  python /mnt/hpccs01/work/microbiome/gnomefish/lara/plasmid_extraction_testing/mda_100cell_pedl_90kb_3kb_gp_4kb_240108/4kb/aviary_complete_updated/.snakemake/scripts/tmp80u12jzh.run_checkm.py' returned non-zero exit status 1.
  File "/mnt/hpccs01/work/microbiome/sw/aviary_repos/aviary-v0.8.3/aviary/aviary/modules/binning/binning.smk", line 419, in __rule_checkm_rosella
  File "/mnt/hpccs01/work/microbiome/conda/envs/aviary-v0.8.3/lib/python3.11/concurrent/futures/thread.py", line 58, in run
Removing output files of failed job checkm_rosella since they might be corrupted:
data/rosella_bins/checkm2_out

Then upon executing the following command: source /mnt/hpccs01/work/microbiome/conda/envs/aviary-v0.8.3/bin/activate '/mnt/hpccs01/work/microbiome/conda/11e1a371ef3335e629225ddf170c50f3_'; set -euo pipefail; python /mnt/hpccs01/work/microbiome/gnomefish/lara/plasmid_extraction_testing/mda_100cell_pedl_90kb_3kb_gp_4kb_240108/4kb/aviary_complete_updated/.snakemake/scripts/tmp80u12jzh.run_checkm.py

The following error message is given: n11115921@cl5n008:/work/microbiome/gnomefish/lara/plasmid_extraction_testing/mda_100cell_pedl_90kb_3kb_gp_4kb_240108/4kb> source /mnt/hpccs01/work/microbiome/conda/envs/aviary-v0.8.3/bin/activate '/mnt/hpccs01/work/microbiome/conda/11e1a371ef3335e629225ddf170c50f3_'; set -euo pipefail; python /mnt/hpccs01/work/microbiome/gnomefish/lara/plasmid_extraction_testing/mda_100cell_pedl_90kb_3kb_gp_4kb_240108/4kb/aviary_complete_updated/.snakemake/scripts/tmp80u12jzh.run_checkm.py python: can't open file '/mnt/hpccs01/work/microbiome/gnomefish/lara/plasmid_extraction_testing/mda_100cell_pedl_90kb_3kb_gp_4kb_240108/4kb/aviary_complete_updated/.snakemake/scripts/tmp80u12jzh.run_checkm.py': [Errno 2] No such file or directory

Thanks :)

aljazdzy commented 5 months ago

Sternp did you ever find a solution to this? I'm having a similar issue.

sternp commented 4 months ago

Sternp did you ever find a solution to this? I'm having a similar issue.

The parameter to avoid the Rosella step is what I'm using for now

aljazdzy commented 4 months ago

Thanks!