Closed hazmup closed 9 months ago
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
@hazmup, how many threads did you assign to the snakemake config?
Issue is stale and will be closed in 7 days unless there is new activity
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.
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:
CARD: v3.2.6 WildCARD: v4.0.0 RGI: v6.0.2