N E X T F L O W ~ version 20.07.1 Launching `nf-core/eager` [nice_tesla] - revision: 29b6e147bd [2.3.1] ---------------------------------------------------- ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/eager v2.3.1 ---------------------------------------------------- Pipeline Name : nf-core/eager Pipeline Version : 2.3.1 Pipeline Release : 2.3.1 Run Name : nice_tesla Input : ibis_screen.tsv Convert input BAM?: No Fasta Ref : /shared/volume/hologenomics/data/avagene/references/bfdv_ref/Beak_and_feather_disease_virus.fasta BAM Index Type : CSI BWA Index : Yes Skipping FASTQC? : Yes Skipping AdapterRemoval?: Yes Running BAM filtering: Yes Skip Read Merging : fastq Run Fastq Host Removal: No Skipping Preseq? : No Skipping Deduplication?: No Skipping DamageProfiler?: No Skipping Qualimap?: No Run BAM Trimming? : No Run PMDtools? : No Run Genotyping? : No Run MultiVCFAnalyzer: No Run VCF2Genome : No Run SexDetErrMine : No Run Nuclear Contamination Estimation: No Run Bedtools Coverage: No Run Metagenomic Binning: No Max Resources : 128 GB memory, 16 cpus, 10d time per job Output Dir : ./results Working Dir : /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work Container Engine : singularity Container : nfcore/eager:2.3.1 Current Home : /groups/hologenomics/avagene Current User : avagene Script Dir : /groups/hologenomics/avagene/.nextflow/assets/nf-core/eager Config Profile : Illumina_nonHalfUDG,hologenomics User : avagene Config Description: Ibis ---------------------------------------------------- Schaffa, Schaffa, Genome Baua! [- ] process > makeFastaIndex - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [a5/fa2852] process > bwa (CHKSEI14060218_SRR7530... [100%] 2 of 2, cached: 2 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [89/fc33f1] process > bwa (CHKSEI14060194_SRR7530... [100%] 3 of 3, cached: 3 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [26/7ccf7f] process > bwa (CHKPEI14080252_SRR7530... [100%] 4 of 4, cached: 4 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [7e/9f9064] process > bwa (CHKPEI14080263_SRR7530... [100%] 8 of 8, cached: 8 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [f6/3f024a] process > bwa (CHKPEI14080279_SRR7530... [100%] 11 of 11, cached: 11 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [b9/854be0] process > bwa (CHKPEI14080274_SRR7530... [100%] 13 of 13, cached: 13 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 [- ] process > get_software_versions - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [e6/44ae14] process > bwa (CHKPEI14080265_SRR7530... [100%] 15 of 15, cached: 15 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [8d/a68e90] process > bwa (CHKPEI14080267_SRR7530... [100%] 17 of 17, cached: 17 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [29/a55e43] process > bwa (CHKPEI14080269_SRR7530... [100%] 20 of 20, cached: 20 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [90/db8bd3] process > bwa (CHKPEI14080264_SRR7530... [100%] 23 of 23, cached: 23 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [36/fc1952] process > bwa (CHKPEI14080255_SRR7530... [100%] 24 of 24, cached: 24 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [9d/d9398e] process > bwa (CHKPEI14080251_SRR7530... [100%] 28 of 28, cached: 28 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [0a/bf3143] process > bwa (CHKPEI14080262_SRR7530... [100%] 31 of 31, cached: 31 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [37/feeb7e] process > bwa (CHKPEI14080270_SRR7530... [100%] 34 of 34, cached: 34 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [95/1a16c6] process > bwa (CHKSEI14060193_SRR7530... [100%] 35 of 35, cached: 35 [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [b6/6ab1cd] process > samtools_flagstat (CHKSEI14... [100%] 3 of 3, cached: 3 [17/2ab489] process > samtools_filter (CHKSEI1406... [100%] 1 of 1, cached: 1 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [7d/04700d] process > samtools_flagstat (CHKPEI14... [100%] 4 of 4, cached: 4 [b7/47d4c8] process > samtools_filter (CHKSEI1406... [100%] 2 of 2, cached: 2 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [74/3c6d27] process > samtools_flagstat (CHKPEI14... [100%] 6 of 6, cached: 6 [b7/47d4c8] process > samtools_filter (CHKSEI1406... [100%] 2 of 2, cached: 2 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [86/42911b] process > samtools_flagstat (CHKSEI14... [100%] 7 of 7, cached: 7 [b7/47d4c8] process > samtools_filter (CHKSEI1406... [100%] 2 of 2, cached: 2 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d6/72996b] process > samtools_flagstat (CHKPEI14... [100%] 10 of 10, cached: 10 [4e/fcfa98] process > samtools_filter (CHKPEI1408... [100%] 5 of 5, cached: 5 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [61/22954b] process > samtools_flagstat (CHKPEI14... [100%] 13 of 13, cached: 13 [bd/0a42b3] process > samtools_filter (CHKPEI1408... [100%] 9 of 9, cached: 9 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [70/5f3cb2] process > samtools_flagstat (CHKPEI14... [100%] 17 of 17, cached: 17 [db/6d1828] process > samtools_filter (CHKPEI1408... [100%] 12 of 12, cached: 12 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [93/61084e] process > samtools_flagstat (CHKSEI14... [100%] 22 of 22, cached: 22 [fa/c046ab] process > samtools_filter (CHKPEI1408... [100%] 15 of 15, cached: 15 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d9/6eb2ed] process > samtools_flagstat (CHKPEI14... [100%] 26 of 26, cached: 26 [65/6218bf] process > samtools_filter (CHKPEI1408... [100%] 17 of 17, cached: 17 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [cb/626d0a] process > samtools_flagstat (CHKPEI14... [100%] 32 of 32, cached: 32 [f4/21c507] process > samtools_filter (CHKPEI1408... [100%] 21 of 21, cached: 21 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [c5/efcdcb] process > samtools_filter (CHKPEI1408... [100%] 26 of 26, cached: 26 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [87/7ea66c] process > samtools_filter (CHKPEI1408... [100%] 30 of 30, cached: 30 [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [ab/2596f5] process > samtools_filter (CHKPEI1408... [100%] 32 of 32, cached: 32 [25/916ff4] process > samtools_flagstat_after_fil... [100%] 2 of 2, cached: 2 [- ] process > endorSpy - [- ] process > dedup - [04/a255b7] process > markduplicates (CHKSEI14060... [100%] 1 of 1, cached: 1 [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [0c/622e8e] process > samtools_filter (CHKPEI1408... [100%] 33 of 33, cached: 33 [9a/8db01a] process > samtools_flagstat_after_fil... [100%] 4 of 4, cached: 4 [- ] process > endorSpy - [- ] process > dedup - [97/feaf3e] process > markduplicates (CHKSEI14060... [100%] 3 of 3, cached: 3 [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [07/585cb3] process > samtools_filter (CHKSEI1406... [100%] 35 of 35, cached: 35 [cd/cdaf9a] process > samtools_flagstat_after_fil... [100%] 7 of 7, cached: 7 [- ] process > endorSpy - [- ] process > dedup - [a4/84e9ff] process > markduplicates (CHKSEI14060... [100%] 6 of 6, cached: 6 [- ] process > library_merge - [44/d68923] process > preseq (CHKSEI14060212_SRR7... [100%] 6 of 6, cached: 6 [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [f4/cc72f6] process > samtools_flagstat_after_fil... [100%] 11 of 11, cached: 11 [- ] process > endorSpy - [- ] process > dedup - [0a/9536a7] process > markduplicates (CHKSEI14060... [100%] 11 of 11, cached: 11 [- ] process > library_merge - [72/9979a1] process > preseq (CHKPEI14080279_SRR7... [100%] 12 of 12, cached: 12 [- ] process > bedtools - [4e/7cd9b1] process > damageprofiler (CHKSEI14060... [100%] 2 of 2, cached: 2 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [68/59c3c3] process > samtools_flagstat_after_fil... [100%] 12 of 12, cached: 12 [- ] process > endorSpy - [- ] process > dedup - [70/a27bd6] process > markduplicates (CHKPEI14080... [100%] 12 of 12, cached: 12 [- ] process > library_merge - [37/df5605] process > preseq (CHKPEI14080267_SRR7... [100%] 15 of 15, cached: 15 [- ] process > bedtools - [bf/a0705a] process > damageprofiler (CHKPEI14080... [100%] 4 of 4, cached: 4 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [49/e1bd20] process > samtools_flagstat_after_fil... [100%] 16 of 16, cached: 16 [- ] process > endorSpy - [- ] process > dedup - [83/c70e2f] process > markduplicates (CHKPEI14080... [100%] 15 of 15, cached: 15 [- ] process > library_merge - [83/fb6ab2] process > preseq (CHKPEI14080260_SRR7... [100%] 20 of 20, cached: 20 [- ] process > bedtools - [56/b382d0] process > damageprofiler (CHKSEI14060... [100%] 6 of 6, cached: 6 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [72/b5f2fd] process > samtools_flagstat_after_fil... [100%] 18 of 18, cached: 18 [- ] process > endorSpy - [- ] process > dedup - [85/c66792] process > markduplicates (CHKPEI14080... [100%] 18 of 18, cached: 18 [- ] process > library_merge - [94/881d0c] process > preseq (CHKPEI14080255_SRR7... [100%] 25 of 25, cached: 25 [- ] process > bedtools - [4b/5a572c] process > damageprofiler (CHKPEI14080... [100%] 8 of 8, cached: 8 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [ef/0649c7] process > samtools_flagstat_after_fil... [100%] 21 of 21, cached: 21 [- ] process > endorSpy - [- ] process > dedup - [e6/5c3d57] process > markduplicates (CHKPEI14080... [100%] 21 of 21, cached: 21 [- ] process > library_merge - [b0/fda961] process > preseq (CHKPEI14080256_SRR7... [100%] 29 of 29, cached: 29 [- ] process > bedtools - [a4/aea038] process > damageprofiler (CHKPEI14080... [100%] 10 of 10, cached: 10 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [b4/56d353] process > samtools_flagstat_after_fil... [100%] 25 of 25, cached: 25 [- ] process > endorSpy - [- ] process > dedup - [5c/3b0244] process > markduplicates (CHKPEI14080... [100%] 25 of 25, cached: 25 [- ] process > library_merge - [cc/235508] process > preseq (CHKSEI14060193_SRR7... [100%] 35 of 35, cached: 35 [- ] process > bedtools - [e0/d24822] process > damageprofiler (CHKPEI14080... [100%] 13 of 13, cached: 13 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [7c/dbb871] process > samtools_flagstat_after_fil... [100%] 30 of 30, cached: 30 [- ] process > endorSpy - [- ] process > dedup - [2e/4d36a5] process > markduplicates (CHKPEI14080... [100%] 28 of 28, cached: 28 [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [af/a38a5f] process > damageprofiler (CHKPEI14080... [100%] 15 of 15, cached: 15 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [a3/d4f685] process > samtools_flagstat_after_fil... [100%] 34 of 34, cached: 34 [- ] process > endorSpy - [- ] process > dedup - [e8/b2ac46] process > markduplicates (CHKPEI14080... [100%] 31 of 31, cached: 31 [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [85/77d07a] process > damageprofiler (CHKPEI14080... [100%] 17 of 17, cached: 17 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [d3/5db62a] process > markduplicates (CHKSEI14060... [100%] 35 of 35, cached: 35 [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [e7/67a3f6] process > damageprofiler (CHKPEI14080... [100%] 20 of 20, cached: 20 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [43/604e54] process > damageprofiler (CHKPEI14080... [100%] 22 of 22, cached: 22 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [b0/6d27cd] process > damageprofiler (CHKPEI14080... [100%] 26 of 26, cached: 26 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [dc/105164] process > damageprofiler (CHKPEI14080... [100%] 31 of 31, cached: 31 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap [ 0%] 0 of 3 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [03/e504d3] process > damageprofiler (CHKSEI14060... [100%] 35 of 35, cached: 35 [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap [ 0%] 0 of 6 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (1) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [a3/c6e020] process > qualimap (CHKSEI14060218_SR... [ 0%] 0 of 8 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (2) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [a3/c6e020] process > qualimap (CHKSEI14060218_SR... [ 0%] 0 of 13 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f4/b5a09a] process > qualimap (CHKSEI14060198_SR... [ 0%] 0 of 20 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f4/b5a09a] process > qualimap (CHKSEI14060198_SR... [ 0%] 0 of 23 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (4) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [04/9c9544] process > qualimap (CHKSEI14060194_SR... [ 0%] 0 of 28 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (4) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [04/9c9544] process > qualimap (CHKSEI14060194_SR... [ 0%] 0 of 32 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (5) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [5a/8415a2] process > qualimap (CHKPEI14080275_SR... [ 0%] 0 of 37 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (6) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [fa/3d3b83] process > qualimap (CHKPEI14080252_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (6) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [fa/3d3b83] process > qualimap (CHKPEI14080252_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (7) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [4d/1a6c72] process > qualimap (CHKSEI14060212_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (8) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [1e/0a3e2c] process > qualimap (CHKPEI14080280_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (8) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [1e/0a3e2c] process > qualimap (CHKPEI14080280_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (8) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [1e/0a3e2c] process > qualimap (CHKPEI14080280_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (9) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [64/e1d1d3] process > qualimap (CHKPEI14080276_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (9) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [64/e1d1d3] process > qualimap (CHKPEI14080276_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (9) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [64/e1d1d3] process > qualimap (CHKPEI14080276_SR... [ 0%] 0 of 38 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (9) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f6/415128] process > qualimap (CHKPEI14080250_SR... [ 3%] 1 of 38, failed: 1 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f6/415128] process > qualimap (CHKPEI14080250_SR... [ 3%] 1 of 38, failed: 1 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f6/415128] process > qualimap (CHKPEI14080250_SR... [ 5%] 2 of 38, failed: 2 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [f4/b5a09a] process > qualimap (CHKSEI14060198_SR... [ 8%] 3 of 38, failed: 3 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [4d/1a6c72] process > qualimap (CHKSEI14060212_SR... [ 18%] 7 of 38, failed: 7 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [1e/0a3e2c] process > qualimap (CHKPEI14080280_SR... [ 24%] 9 of 38, failed: 9 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/I80GmUEqpqyHb executor > slurm (10) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [- ] process > fastqc - [- ] process > fastp - [- ] process > adapter_removal - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [99/0eceaa] process > bwa (CHKSEI14060195_SRR7530... [100%] 38 of 38, cached:... [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [d1/97c009] process > samtools_flagstat (CHKSEI14... [100%] 38 of 38, cached:... [29/e15a54] process > samtools_filter (CHKSEI1406... [100%] 38 of 38, cached:... [52/395cfb] process > samtools_flagstat_after_fil... [100%] 38 of 38, cached:... [- ] process > endorSpy - [- ] process > dedup - [1c/ab4426] process > markduplicates (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > library_merge - [82/6e13fd] process > preseq (CHKSEI14060195_SRR7... [100%] 38 of 38, cached:... [- ] process > bedtools - [ef/a2a5bd] process > damageprofiler (CHKSEI14060... [100%] 38 of 38, cached:... [- ] process > mapdamage_rescaling - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [1e/0a3e2c] process > qualimap (CHKPEI14080280_SR... [ 24%] 9 of 38, failed: 9 [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sex_deterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [e6/343a4d] process > output_documentation [100%] 1 of 1, cached: 1 ✔ [fb/7f049e] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > multiqc [ 0%] 0 of 1 Error executing process > 'qualimap (CHKPEI14080276_SRR7530219)' Caused by: Process `qualimap (CHKPEI14080276_SRR7530219)` terminated with an error exit status (255) Command executed: qualimap bamqc -bam CHKPEI14080276_SRR7530219_rmdup.bam -nt 2 -outdir . -outformat "HTML" --java-mem-size=4G Command exit status: 255 Command output: Java memory size is set to 4G Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 32 Max memory (Mb): 3817 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 399 Chunk of reads size: 1000 Number of threads: 2 Processed 50 out of 399 windows... Processed 100 out of 399 windows... Processed 150 out of 399 windows... Processed 200 out of 399 windows... Processed 250 out of 399 windows... Processed 300 out of 399 windows... Processed 350 out of 399 windows... Total processed windows:399 Number of reads: 0 Number of valid reads: 0 Number of correct strand reads:0 Inside of regions... Num mapped reads: 0 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 0 Wed Jan 20 00:56:26 UTC 2021 WARNING Cleanup output dir Command error: Failed to run bamqc java.lang.RuntimeException: The BAM file is empty or corrupt at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:529) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113) Work dir: /shared/volume/hologenomics/data/avagene/museuomics/ibis/eager/bfdv_mapping_190121/work/64/e1d1d3c67c3a0d266d6751e10ed248 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`