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Hi, I am trying to run the pipeline with command " snakemake -j 30 variants --configfile config.yml" and I have a directory with my long reads fastq.gz files, I am getting this error:
Error in rule filter_reads:
jobid: 10
input: pteres
output: cyp51A_read_run/read.filt.fastq.gz, cyp51A_read_run/09_stats/01_reads_stats.txt
shell:
printf 'Total reads in file pre filtering: ' 2>&1 | tee cyp51A_read_run/09_stats/01_reads_stats.txt
if [[ pteres =~ \.gz$ ]]
then
zcat pteres | echo $((`wc -l`/4)) 2>&1 | tee -a cyp51A_read_run/09_stats/01_reads_stats.txt
else
cat pteres | echo $((`wc -l`/4)) 2>&1 | tee -a cyp51A_read_run/09_stats/01_reads_stats.txt
fi
if [[ True == "True" ]]
then
filtlong --min_length 200 --min_mean_q 50 pteres | gzip > cyp51A_read_run/read.filt.fastq.gz
printf 'Total reads in file post filtering: ' 2>&1 | tee -a cyp51A_read_run/09_stats/01_reads_stats.txt
zcat cyp51A_read_run/read.filt.fastq.gz | echo $((`wc -l`/4)) 2>&1 | tee -a cyp51A_read_run/09_stats/01_reads_stats.txt
else
cp pteres cyp51A_read_run/read.filt.fastq.gz
fi
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Thanks!
The text was updated successfully, but these errors were encountered:
Hi, I am trying to run the pipeline with command " snakemake -j 30 variants --configfile config.yml" and I have a directory with my long reads fastq.gz files, I am getting this error:
Error in rule filter_reads:
jobid: 10
input: pteres
output: cyp51A_read_run/read.filt.fastq.gz, cyp51A_read_run/09_stats/01_reads_stats.txt
shell:
Thanks!
The text was updated successfully, but these errors were encountered: