NiccoloBassetti
commented
1 year ago Hi @kcl58759, do you still need help with this? I had the same issue and this solution worked for me. Following the example, I created a config file name "config.mysample.json". And as spid I simply used "mysample" (or any string between "config." and ".json").
Can you try if this works for you too?
I am having some trouble running the code. Namely, I keep getting the error run_purge_dups.py: error: unrecognized arguments: spid I read I could make up my own spid so i have tried a few different things but to no avail.
Here is my configuration file and my run_purge_dups command.
Configuration file:
{ "cc": { "fofn": "./pb.fofn", "isdip": 1, "core": 12, "mem": 20000, "queue": "normal", "mnmp_opt": "", "bwa_opt": "", "ispb": 1, "skip": 0 }, "sa": { "core": 12, "mem": 10000, "queue": "normal" }, "busco": { "core": 12, "mem": 20000, "queue": "long", "skip": 0, "lineage": "hypocreales", "prefix": "1033_HiCanu_CCS.contigs_purged", "tmpdir": "busco_tmp" }, "pd": { "mem": 20000, "queue": "normal" }, "gs": { "mem": 10000, "oe": 1 }, "kcp": { "core": 12, "mem": 30000, "fofn": "", "prefix": "1033_HiCanu_CCS.contigs_purged_kcm", "tmpdir": "kcp_tmp", "skip": 1 }, "ref": "/scratch/kcl58759/Eco_pacbio_kendall/1033_HiCanu_CCS.contigs.fasta", "out_dir": "1033_HiCanu_CCS.contigs" }
Run_purge_dups command (submitting to UGA cluster)
!/bin/bash
SBATCH --job-name=run_purge_dups
SBATCH --partition=batch
SBATCH --ntasks=5
SBATCH --cpus-per-task=1
SBATCH --mem=80gb
SBATCH --time=99:00:00
SBATCH --output=runpurge.out
SBATCH --error=runpurge.err
SBATCH --mail-user=kcl58759@uga.edu
SBATCH --mail-type=END,FAIL
ml Purge_dups/1.2.5-foss-2019b-Python-3.8.2
cd /scratch/kcl58759/Eco_pacbio_kendall/
run_purge_dups.py 1033_HiCanu_CCS.contigs.fasta 1033_purgedups src spid