[BUG] rgi bwt does not use threads, seems to hang

[hazmup]

I am running rgi bwt on a SLURM cluster through a snakemake pipeline. I have set it to use 40 threads, but it shows as only 2 are being used. Also it has taken 16 hours so far for a single metagenomic sample and I do not know if it has stalled.

rgi bwt --read_one R1_clean.fastq.gz --read_two R2_clean.fastq.gz --aligner kma --threads 40 --output_file S1.txt --include_wildcard --include_other_models --local

Input is paired metagenomic fastq.gz files, around 4GB each. Some other samples (not yet tried), are about 15GB each.

This is part of the status report:

State: RUNNING
Nodes: 1
Cores per node: 2
CPU Utilized: 00:00:00
CPU Efficiency: 0.00% of 1-08:17:26 core-walltime

CARD: v3.2.6 WildCARD: v4.0.0 RGI: v6.0.2

[hazmup]

UPDATE: It actually seems to hang after a while, as there are no changes in any of the output files for hours (see below):

(base) [sgkionis@login02 sgkionis]$ ls rgi/ -alh
total 54G
drwxrwxr-x  2 sgkionis sgkionis 4.0K May  4 21:29 .
drwxrwxrwx 12 sgkionis sgkionis 4.0K May  4 19:29 ..
-rw-rw-r--  1 sgkionis sgkionis 379M May  5 16:22 SD11_S1.txt.coverage.temp.txt
-rw-rw-r--  1 sgkionis sgkionis  22M May  5 16:28 SD11_S1.txt.coverage_all_positions.summary.temp.txt
-rw-rw-r--  1 sgkionis sgkionis  50M May  5 16:28 SD11_S1.txt.coverage_all_positions.temp.txt
-rw-rw-r--  1 sgkionis sgkionis 279M May  5 16:29 SD11_S1.txt.model_species_data_type.temp.txt
-rw-rw-r--  1 sgkionis sgkionis  165 May  5 16:28 SD11_S1.txt.reference_mapping_stats.txt
-rw-rw-r--  1 sgkionis sgkionis 7.9G May  5 16:21 SD11_S1.txt.seqs.temp.txt
-rw-rw-r--  1 sgkionis sgkionis 5.6G May  5 16:14 SD11_S1.txt.sorted.length_100.bam
-rw-rw-r--  1 sgkionis sgkionis 3.8M May  5 16:15 SD11_S1.txt.sorted.length_100.bam.bai
-rw-rw-r--  1 sgkionis sgkionis 5.8G May  5 15:46 SD11_S1.txt.sorted.temp.bam
-rw-rw-r--  1 sgkionis sgkionis 3.8M May  5 15:48 SD11_S1.txt.sorted.temp.bam.bai
-rw-rw-r--  1 sgkionis sgkionis 5.6G May  5 15:42 SD11_S1.txt.temp.bam
-rw-rw-r--  1 sgkionis sgkionis  29G May  5 15:12 SD11_S1.txt.temp.sam
-rw-rw-r--  1 sgkionis sgkionis  30M May  5 15:12 SD11_S1.txt.temp.sam.temp.aln
-rw-rw-r--  1 sgkionis sgkionis  16M May  5 15:12 SD11_S1.txt.temp.sam.temp.frag.gz
-rw-rw-r--  1 sgkionis sgkionis 1.7M May  5 15:12 SD11_S1.txt.temp.sam.temp.fsa
-rw-rw-r--  1 sgkionis sgkionis 638K May  5 15:12 SD11_S1.txt.temp.sam.temp.res
-rw-rw-r--  1 sgkionis sgkionis  36M May  5 15:12 SD11_S1.txt.temp.sam.temp.vcf.gz
-rw-rw-r--  1 sgkionis sgkionis  26M May  5 16:15 SD11_S1.txt.temp.txt

[raphenya]

@hazmup, how many threads did you assign to the snakemake config?

[github-actions[bot]]

Issue is stale and will be closed in 7 days unless there is new activity