I got the following Bowtie2 error:
Error in rule bowtie2_map:
jobid: 8
output: ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.sam, ctrl_mc/logs/bowtie2map.log
shell:
bowtie2-build -o 3 --threads 18 -q ctrl_mc/reference_selection/mc.refseq.fna ctrl_mc/assembly/mc.index 1>> ctrl_mc/assembly/mc.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 18 -x ctrl_mc/assembly/mc.index -q -U ctrl_R1_paired.fastq,ctrl_R2_paired.fastq,ctrl_unpaired.fastq -S ctrl_mc/assembly/mc.sam.all > ctrl_mc/logs/bowtie2map.log 2>&1; python3 /home/modesto/Applications/MetaCompass-2.0-beta/bin/best_strata.py ctrl_mc/assembly/mc.sam.all ctrl_mc/assembly/mc.sam; rm ctrl_mc/assembly/mc.sam.all && touch ctrl_mc/assembly/.run1.ok
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
I just updated all dependencies before using. I tried the 1.12 and 2.0Beta releases and I got the same error. Running on Ubuntu 20.04.1 LTS.
Thanks
I got the following Bowtie2 error:
Error in rule bowtie2_map:
jobid: 8
output: ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.sam, ctrl_mc/logs/bowtie2map.log
shell:
bowtie2-build -o 3 --threads 18 -q ctrl_mc/reference_selection/mc.refseq.fna ctrl_mc/assembly/mc.index 1>> ctrl_mc/assembly/mc.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 18 -x ctrl_mc/assembly/mc.index -q -U ctrl_R1_paired.fastq,ctrl_R2_paired.fastq,ctrl_unpaired.fastq -S ctrl_mc/assembly/mc.sam.all > ctrl_mc/logs/bowtie2map.log 2>&1; python3 /home/modesto/Applications/MetaCompass-2.0-beta/bin/best_strata.py ctrl_mc/assembly/mc.sam.all ctrl_mc/assembly/mc.sam; rm ctrl_mc/assembly/mc.sam.all && touch ctrl_mc/assembly/.run1.ok
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
I just updated all dependencies before using. I tried the 1.12 and 2.0Beta releases and I got the same error. Running on Ubuntu 20.04.1 LTS.
Thanks