N E X T F L O W ~ version 25.10.0 Launching `https://github.com/nf-core/mag` [confident_pesquet] DSL2 - revision: 99859fc04c [main] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/mag 5.2.0 ------------------------------------------------------ Input/output options input : samplesheet.csv outdir : mag_out Generic options trace_report_suffix : 2025-11-27_08-31-20 Taxonomic profiling options gtdbtk_min_completeness : 50.0 gtdbtk_max_contamination: 10.0 Bin quality check options run_busco : true Core Nextflow options revision : main runName : confident_pesquet containerEngine : singularity launchDir : /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm workDir : /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work projectDir : /z/home/pbo/.nextflow/assets/nf-core/mag userName : pbo profile : sge,singularity configFiles : /z/home/pbo/.nextflow/assets/nf-core/mag/nextflow.config, /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The pipeline https://doi.org/10.1093/nargab/lqac007 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/mag/blob/main/CITATIONS.md [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 1 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 8 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 14 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 19 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 20 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED - [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE - [- ] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES - [- ] NFCORE_MAG:MAG:QUAST - [- ] NFCORE_MAG:MAG:PRODIGAL - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 20 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [- ] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS - [- ] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 - [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING - [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [- ] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN - [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER - Plus 20 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 [- ] NFCORE_MAG:MAG:BINNING:MAXBIN2 - [- ] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT - [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 [ae/aab4d8] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 80%] 4 of 5, cached: 4 [- ] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS - [b7/ae6200] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample4) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [b3/863d8e] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample4) [ 75%] 6 of 8, cached: 6 [- ] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS [ 0%] 0 of 2 Plus 17 more processes waiting for tasks… [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [0e/7bc6e7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (FLYE-sample2) [100%] 7 of 7, cached: 7 [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [b7/ae6200] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample4) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [b3/863d8e] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample4) [ 75%] 6 of 8, cached: 6 [d1/da75ee] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (1) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [4a/f1f7a9] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample1) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [b3/863d8e] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample4) [ 75%] 6 of 8, cached: 6 [d1/da75ee] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (2) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [b3/863d8e] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample4) [ 75%] 6 of 8, cached: 6 [d1/da75ee] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (3) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [58/d38f37] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample1) [ 75%] 6 of 8, cached: 6 [d1/da75ee] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (4) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [d1/da75ee] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (5) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (6) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [aa/f40edd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample4) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [c8/e1b6fe] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (7) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [c8/e1b6fe] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (9) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Staging foreign file: https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz executor > sge (9) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (9) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [ 87%] 7 of 8, cached: 7 [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [100%] 7 of 7, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (9) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [91/c523ac] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample1) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (10) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (10) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (10) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 33%] 2 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [100%] 18 of 18, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (10) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [eb/1ea167] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MaxBin2-sample1) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (11) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [ed/c3be67] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample4) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [ 87%] 7 of 8, cached: 7 [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [5b/ac451f] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample2) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [c8/e1b6fe] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [c8/e1b6fe] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [ 90%] 18 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [c8/e1b6fe] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3) [ 66%] 4 of 6, cached: 2 [ed/c3be67] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample4) [ 95%] 19 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 66%] 4 of 6, cached: 2 [ed/c3be67] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample4) [ 95%] 19 of 20, cached: 18 [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [100%] 20 of 20, cached: 18 ✔ [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 75%] 6 of 8, cached: 6 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [100%] 20 of 20, cached: 18 ✔ [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [3e/f61372] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2) [ 87%] 7 of 8, cached: 6, ignored: 1 [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [100%] 20 of 20, cached: 18 ✔ [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… [3e/f61372] NOTE: Process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample2)` terminated with an error exit status (1) -- Error is ignored ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > sge (12) [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED - [- ] NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ - [c0/9cdb48] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample3) [100%] 4 of 4, cached: 4 ✔ [72/8508ff] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample1) [100%] 4 of 4, cached: 4 ✔ [6f/17e44c] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample1) [100%] 4 of 4, cached: 4 ✔ [02/afe1cf] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample3) [100%] 4 of 4, cached: 4 ✔ [12/433539] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample4) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS - [- ] NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES - [- ] NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT - [- ] NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID - [f6/919299] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample1) [100%] 4 of 4, cached: 4 ✔ [8b/e12ebc] NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample3) [100%] 4 of 4, cached: 4 ✔ [- ] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES - [59/089add] NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample1.assembly.fasta.gz) [100%] 8 of 8, cached: 8 ✔ [54/ff8b99] NFCORE_MAG:MAG:QUAST (FLYE-sample1) [100%] 8 of 8, cached: 8 ✔ [f9/174633] NFCORE_MAG:MAG:PRODIGAL (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD - [- ] NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN - [a9/8015da] NFC…MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (7) [100%] 8 of 8, cached: 8 ✔ [fb/b68b8a] NFC…G:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample3) [100%] 32 of 32, cached: 32 ✔ [80/a05f29] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample3) [100%] 8 of 8, cached: 8 ✔ [- ] NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD - [3c/8e0133] NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample1) [100%] 8 of 8, cached: 8 ✔ [87/71621c] NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample3) [100%] 8 of 8, cached: 8 ✔ [5b/88c6c6] NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample1) [100%] 8 of 8, cached: 8 ✔ [e0/547bd7] NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (METAMDBG-sample1) [100%] 8 of 8, cached: 8 ✔ [13/7721cd] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample3) [100%] 8 of 8, cached: 8 ✔ [08/1cec14] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample1) [100%] 8 of 8, cached: 8 ✔ [35/afc7e2] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample3) [100%] 8 of 8, cached: 8 ✔ [8c/d7f6a0] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample2) [100%] 8 of 8, cached: 7 ✔ [56/06d170] NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample2) [100%] 8 of 8, cached: 7 ✔ [92/651229] NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample2) [ 75%] 6 of 8, cached: 6 [f7/35d5e9] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample2) [100%] 8 of 8, cached: 8 ✔ [96/b5baf5] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample4) [100%] 8 of 8, cached: 8 ✔ [58/d38f37] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample1) [100%] 8 of 8, cached: 6, ignored: 2 ✔ [42/2607d1] NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample4) [ 66%] 4 of 6, cached: 2 [51/54e834] NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (FLYE-MetaBinner-sample2) [100%] 20 of 20, cached: 18 ✔ [59/a440d4] NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MaxBin2-sample2.noclass.1.fa.gz) [100%] 22 of 22, cached: 22 Plus 15 more processes waiting for tasks… [58/d38f37] NOTE: Process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample1)` terminated with an error exit status (1) -- Error is ignored ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)' Caused by: Missing output file(s) `*.tooShort.fa.gz` expected by process `NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample3)` Command executed: # unzip membership file zcat METAMDBG-MetaBinner-sample3.tsv.gz > membership.tsv # collect bins & un-binned fractions create_metabinner_bins.py \ membership.tsv \ METAMDBG-sample3.contigs.fasta \ ./bins \ METAMDBG-MetaBinner-sample3 \ 1500 find ./bins/ -name "*.fa" -type f | xargs -t -n 1 bgzip -@ 2 # zip contig fractions find ./bins/ -name "*[tooShort,unbinned].fa.gz" -type f -exec mv {} . \; cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS": python: $(python --version 2>&1 | sed 's/Python //g') END_VERSIONS Command exit status: 0 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.7.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.18.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.14.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.12.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.2.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.15.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.8.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.13.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.11.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.16.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.1.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.4.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.unbinned.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.17.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.10.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.3.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.5.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.6.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.19.fa bgzip -@ 2 ./bins/METAMDBG-MetaBinner-sample3.9.fa Work dir: /net/nfs-ds.sdma.nzcorp.net/srv/nfs/datasets/ds_mr_metagenome/proj/fecalferm/work/c8/e1b6fefb883aeacebb83f08405abaa Container: /z/datasets/ds_mr_metagenome/nfcore_pipelines/depot.galaxyproject.org-singularity-metabinner-1.4.4--hdfd78af_0.img Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details