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Error in rule filter_reads: #39

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Rabisazia1 opened this issue Nov 14, 2024 · 0 comments
Open

Error in rule filter_reads: #39

Rabisazia1 opened this issue Nov 14, 2024 · 0 comments

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@Rabisazia1
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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!

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