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GW-HIVE / CensuScope

CensuScope is designed and optimized for the quick detection of the components in a given NGS metagenomic dataset and provides users with a standard format report of components into species or higher taxonomic node resolution.
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test CensuScope on pegasus #4

Open penningtonea opened 1 week ago

penningtonea commented 1 week ago

Test censuscope on pegasus using NT and slimNT.

penningtonea commented 1 week ago

bash script: 

#!/bin/bash
#SBATCH -p defq -t 1:00:000
module load python3
module load blast+
cd /SMHS/groups/hivelab/epennington/CensuScope
srun lib/censuscope.py -i 1 -s 1000 -t species -q SRR9176576_1.fastq -d /SMHS/groups/hivelab/NT
penningtonea commented 1 week ago

ran above code and got the following output:

image

SUMMARY job failed with error /bin/sh: seqtk: command not found

penningtonea commented 1 week ago

Checked and adjusted permissions for input files, scripts, and database with chmod +x [files] and got same error message. Switching input file to >NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome fasta file to avoid seqtk function