Nextflow workflow report

`[golden_heyrovsky]` (resumed run)

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

SIGINT

Run times

04-Dec-2024 10:10:37 - 04-Dec-2024 10:13:51 (duration: 3m 14s)

0 succeeded

65 cached

0 ignored

0 failed

Nextflow command

nextflow run nf-core/methylseq -c /gscratch/scrubbed/strigg/analyses/20241127_methylseq/uw_hyak_strigg.config --input /gscratch/scrubbed/strigg/analyses/20241127_methylseq/samplesheet.csv --outdir /gscratch/scrubbed/strigg/analyses/20241127_methylseq --fasta /gscratch/scrubbed/sr320/github/ceasmallr/data/genome/Cvirginica_v300.fa -resume -with-report nf_report.html -with-trace -with-timeline nf_timeline.html

CPU-Hours: 395.8 (100% cached)
Launch directory: /mmfs1/gscratch/scrubbed/strigg/analyses/20241127_methylseq
Work directory: /mmfs1/gscratch/scrubbed/strigg/analyses/20241127_methylseq/work
Project directory: /mmfs1/home/strigg/.nextflow/assets/nf-core/methylseq
Script name: main.nf
Script ID: 78f1f08d9049bd123f3defd84fae2dbc
Workflow session: 45487f00-b0f5-4b86-af8f-bc259e96f62a
Workflow repository: https://github.com/nf-core/methylseq, revision master (commit hash d16f8f81e812d86f4d297e69de3f001628dfd5b4)
Workflow profile: standard
Nextflow version: version 24.10.1, build 5930 (18-11-2024 12:21 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Raw Usage
% Allocated

Memory

Job Duration

Raw Usage
% Allocated

I/O

Read
Write

Tasks

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task_id	process	tag	status	hash	allocated cpus	%cpu	allocated memory	%mem	vmem	rss	peak_vmem	peak_rss	allocated time	duration	realtime	script	exit	submit	start	complete	rchar	wchar	syscr	syscw	read_bytes	write_bytes	native_id	name	module	container	disk	attempt	scratch	workdir


bismark_genome_preparation \
        --bowtie2 \
        BismarkIndex

    rm BismarkIndex/Cvirginica_v300.fa

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION":
        bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
    END_VERSIONS
printf "%s %s\n" CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz CF01-CM01-Zygote_1.gz CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz CF01-CM01-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF01-CM01-Zygote_1.gz CF01-CM01-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
[ ! -f  CF01-CM01-Zygote_1.fastq.gz ] && ln -s CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz CF01-CM01-Zygote_1.fastq.gz
        [ ! -f  CF01-CM01-Zygote_2.fastq.gz ] && ln -s CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz CF01-CM01-Zygote_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF01-CM01-Zygote_1.fastq.gz \
            CF01-CM01-Zygote_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
[ ! -f  CF01-CM02-Larvae_1.fastq.gz ] && ln -s CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz CF01-CM02-Larvae_1.fastq.gz
        [ ! -f  CF01-CM02-Larvae_2.fastq.gz ] && ln -s CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF01-CM02-Larvae_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF01-CM02-Larvae_1.fastq.gz \
            CF01-CM02-Larvae_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
printf "%s %s\n" CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz CF01-CM02-Larvae_1.gz CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF01-CM02-Larvae_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF01-CM02-Larvae_1.gz CF01-CM02-Larvae_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
printf "%s %s\n" CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz CF02-CM02-Zygote_1.gz CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz CF02-CM02-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF02-CM02-Zygote_1.gz CF02-CM02-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
[ ! -f  CF02-CM02-Zygote_1.fastq.gz ] && ln -s CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz CF02-CM02-Zygote_1.fastq.gz
        [ ! -f  CF02-CM02-Zygote_2.fastq.gz ] && ln -s CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz CF02-CM02-Zygote_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF02-CM02-Zygote_1.fastq.gz \
            CF02-CM02-Zygote_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
printf "%s %s\n" CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz CF03-CM03-Zygote_1.gz CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz CF03-CM03-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF03-CM03-Zygote_1.gz CF03-CM03-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
printf "%s %s\n" CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz CF03-CM04-Larvae_1.gz CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz CF03-CM04-Larvae_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF03-CM04-Larvae_1.gz CF03-CM04-Larvae_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
ln -sf $(readlink Cvirginica_v300.fa) BismarkIndex/Cvirginica_v300.fa

    bismark \
        -1 CF01-CM01-Zygote_1_val_1.fq.gz -2 CF01-CM01-Zygote_2_val_2.fq.gz \
        --genome BismarkIndex \
        --bam \
        --bowtie2 --multicore 4

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
        bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
    END_VERSIONS
ln -sf $(readlink Cvirginica_v300.fa) BismarkIndex/Cvirginica_v300.fa

    bismark \
        -1 CF01-CM02-Larvae_1_val_1.fq.gz -2 CF01-CM02-Larvae_2_val_2.fq.gz \
        --genome BismarkIndex \
        --bam \
        --bowtie2 --multicore 4

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
        bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
    END_VERSIONS
printf "%s %s\n" CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz CF03-CM05-Larvae_1.gz CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz CF03-CM05-Larvae_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF03-CM05-Larvae_1.gz CF03-CM05-Larvae_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
[ ! -f  CF03-CM03-Zygote_1.fastq.gz ] && ln -s CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz CF03-CM03-Zygote_1.fastq.gz
        [ ! -f  CF03-CM03-Zygote_2.fastq.gz ] && ln -s CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz CF03-CM03-Zygote_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF03-CM03-Zygote_1.fastq.gz \
            CF03-CM03-Zygote_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
printf "%s %s\n" CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz CF04-CM04-Zygote_1.gz CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz CF04-CM04-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF04-CM04-Zygote_1.gz CF04-CM04-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
printf "%s %s\n" CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz CF05-CM02-Larvae_1.gz CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF05-CM02-Larvae_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF05-CM02-Larvae_1.gz CF05-CM02-Larvae_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
printf "%s %s\n" CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz CF05-CM05-Zygote_1.gz CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz CF05-CM05-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF05-CM05-Zygote_1.gz CF05-CM05-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
ln -sf $(readlink Cvirginica_v300.fa) BismarkIndex/Cvirginica_v300.fa

    bismark \
        -1 CF02-CM02-Zygote_1_val_1.fq.gz -2 CF02-CM02-Zygote_2_val_2.fq.gz \
        --genome BismarkIndex \
        --bam \
        --bowtie2 --multicore 4

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
        bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
    END_VERSIONS
[ ! -f  CF03-CM04-Larvae_1.fastq.gz ] && ln -s CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz CF03-CM04-Larvae_1.fastq.gz
        [ ! -f  CF03-CM04-Larvae_2.fastq.gz ] && ln -s CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz CF03-CM04-Larvae_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF03-CM04-Larvae_1.fastq.gz \
            CF03-CM04-Larvae_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
printf "%s %s\n" CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz CF06-CM01-Zygote_1.gz CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz CF06-CM01-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF06-CM01-Zygote_1.gz CF06-CM01-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
[ ! -f  CF03-CM05-Larvae_1.fastq.gz ] && ln -s CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz CF03-CM05-Larvae_1.fastq.gz
        [ ! -f  CF03-CM05-Larvae_2.fastq.gz ] && ln -s CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz CF03-CM05-Larvae_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF03-CM05-Larvae_1.fastq.gz \
            CF03-CM05-Larvae_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
printf "%s %s\n" CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz CF06-CM02-Larvae_1.gz CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF06-CM02-Larvae_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF06-CM02-Larvae_1.gz CF06-CM02-Larvae_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
printf "%s %s\n" CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz CF07-CM02-Zygote_1.gz CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz CF07-CM02-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF07-CM02-Zygote_1.gz CF07-CM02-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS
[ ! -f  CF04-CM04-Zygote_1.fastq.gz ] && ln -s CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz CF04-CM04-Zygote_1.fastq.gz
        [ ! -f  CF04-CM04-Zygote_2.fastq.gz ] && ln -s CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz CF04-CM04-Zygote_2.fastq.gz
        trim_galore \
            --fastqc \
            --cores 8 \
            --paired \
            --gzip \
            CF04-CM04-Zygote_1.fastq.gz \
            CF04-CM04-Zygote_2.fastq.gz

        cat <<-END_VERSIONS > versions.yml
        "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
            trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
            cutadapt: $(cutadapt --version)
        END_VERSIONS
ln -sf $(readlink Cvirginica_v300.fa) BismarkIndex/Cvirginica_v300.fa

    bismark \
        -1 CF03-CM04-Larvae_1_val_1.fq.gz -2 CF03-CM04-Larvae_2_val_2.fq.gz \
        --genome BismarkIndex \
        --bam \
        --bowtie2 --multicore 4

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
        bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
    END_VERSIONS
printf "%s %s\n" CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz CF08-CM03-Zygote_1.gz CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz CF08-CM03-Zygote_2.gz | while read old_name new_name; do
        [ -f "${new_name}" ] || ln -s $old_name $new_name
    done

    fastqc \
        --quiet \
        --threads 6 \
        --memory 6144 \
        CF08-CM03-Zygote_1.gz CF08-CM03-Zygote_2.gz

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
        fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
    END_VERSIONS

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