Hii, I am stuck in the nf-core at one point same error given below I am getting kindly suggest what to do with this error and how I can solve it /hdd3/nfcore-eager_test$ ./nextflow run nf-core/eager -r 2.5.1 -profile conda --input '/hdd3/Archeomics/es1/*_R{1,2}.fastq.gz' --fasta '/hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa' --bwa_index '/hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/' --fasta_index '/hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai' --seq_dict '/hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.dict' --outdir '/hdd3/results_conda_es1/' N E X T F L O W ~ version 22.10.4 Launching `https://github.com/nf-core/eager` [curious_swirles] DSL1 - revision: 4eb0ffea9d [2.5.1] ------------------------------------------------------ ,--./,-. _ _ _ __ _ /,-._.--~' |\ | |__ _ / ` / \ |_) |__ } { | \| | \__, \__/ | \ |___ \`-._,-

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.,.,' nf-core/eager v2.5.1 ------------------------------------------------------ No TSV file provided - creating TSV from supplied directory. Reading path(s): /hdd3/Archeomics/es1/*_R{1,2}.fastq.gz Generating paired-end FASTQ data TSV Core Nextflow options revision : 2.5.1 runName : curious_swirles container : nfcore/eager:2.5.1 launchDir : /hdd3/nfcore-eager_test workDir : /hdd3/nfcore-eager_test/work projectDir : /home/user/.nextflow/assets/nf-core/eager userName : user profile : conda configFiles : /home/user/.nextflow/assets/nf-core/eager/nextflow.config Input/output options input : /hdd3/Archeomics/es1/*_R{1,2}.fastq.gz Reference genome options fasta : /hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa igenomes_base : s3://ngi-igenomes/igenomes/ igenomes_ignore : true bwa_index : /hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/ fasta_index : /hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai seq_dict : /hdd3/Archeomics/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.dict Output options outdir : /hdd3/results_conda_es1/ Generic options max_multiqc_email_size: 25 MB schema_ignore_params : genomes,input_paths Max job request options max_memory : 128 GB max_time : 10d ------------------------------------------------------ Only displaying parameters that differ from defaults. ------------------------------------------------------ Schaffa, Schaffa, Genome Baua! executor > local (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [8e/656fcf] process > fastqc (ES1_L0) [ 0%] 0 of 1 [- ] process > fastp - [f9/552ba4] process > adapter_removal (ES1_L0) [ 0%] 0 of 1 [- ] process > post_ar_fastq_trimming - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_calculation - [- ] process > mapdamage_rescaling - [- ] process > mask_reference_for_pmdtools - executor > local (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [8e/656fcf] process > fastqc (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > fastp - [f9/552ba4] process > adapter_removal (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > post_ar_fastq_trimming - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_calculation - [- ] process > mapdamage_rescaling - [- ] process > mask_reference_for_pmdtools - [- ] process > pmdtools - [- ] process > bam_trim - executor > local (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [8e/656fcf] process > fastqc (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > fastp - [f9/552ba4] process > adapter_removal (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > post_ar_fastq_trimming - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_calculation - [- ] process > mapdamage_rescaling - [- ] process > mask_reference_for_pmdtools - [- ] process > pmdtools - [- ] process > bam_trim - executor > local (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [8e/656fcf] process > fastqc (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > fastp - [f9/552ba4] process > adapter_removal (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > post_ar_fastq_trimming - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_calculation - [- ] process > mapdamage_rescaling - [- ] process > mask_reference_for_pmdtools - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - executor > local (3) [- ] process > makeFastaIndex - [- ] process > makeSeqDict - [- ] process > convertBam - [- ] process > indexinputbam - [8e/656fcf] process > fastqc (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > fastp - [f9/552ba4] process > adapter_removal (ES1_L0) [100%] 1 of 1, failed: 1 ✘ [- ] process > post_ar_fastq_trimming - [- ] process > lanemerge - [- ] process > lanemerge_hostremoval_fastq - [- ] process > fastqc_after_clipping - [- ] process > bwa - [- ] process > bwamem - [- ] process > circulargenerator - [- ] process > circularmapper - [- ] process > bowtie2 - [- ] process > hostremoval_input_fastq - [- ] process > seqtype_merge - [- ] process > samtools_flagstat - [- ] process > samtools_filter - [- ] process > samtools_flagstat_after_filter - [- ] process > endorSpy - [- ] process > dedup - [- ] process > markduplicates - [- ] process > library_merge - [- ] process > preseq - [- ] process > bedtools - [- ] process > damageprofiler - [- ] process > mapdamage_calculation - [- ] process > mapdamage_rescaling - [- ] process > mask_reference_for_pmdtools - [- ] process > pmdtools - [- ] process > bam_trim - [- ] process > additional_library_merge - [- ] process > qualimap - [- ] process > picard_addorreplacereadgroups - [- ] process > genotyping_ug - [- ] process > genotyping_hc - [- ] process > genotyping_freebayes - [- ] process > genotyping_pileupcaller - [- ] process > eigenstrat_snp_coverage - [- ] process > genotyping_angsd - [- ] process > bcftools_stats - [- ] process > vcf2genome - [- ] process > multivcfanalyzer - [- ] process > mtnucratio - [- ] process > sexdeterrmine_prep - [- ] process > sexdeterrmine - [- ] process > nuclear_contamination - [- ] process > print_nuclear_contamination - [- ] process > metagenomic_complexity_filter - [- ] process > malt - [- ] process > maltextract - [- ] process > kraken - [- ] process > kraken_parse - [- ] process > kraken_merge - [- ] process > output_documentation [ 0%] 0 of 1 [a4/4e642c] process > get_software_versions [100%] 1 of 1 [- ] process > multiqc - Execution cancelled -- Finishing pending tasks before exit -[nf-core/eager] Pipeline completed with errors- Error executing process > 'fastqc (ES1_L0)' Caused by: Process

fastqc (ES1_L0)

terminated with an error exit status (127) Command executed: fastqc -t 2 -q ES1_R1.fastq.gz ES1_R2.fastq.gz rename 's/_fastqc\.zip$/_raw_fastqc.zip/' *_fastqc.zip rename 's/_fastqc\.html$/_raw_fastqc.html/' *_fastqc.html Command exit status: 127 Command output: (empty) Command error: .command.sh: line 2: fastqc: command not found

I see this is an error in #CEQBS091V, best to ask on the #CEQBS091V channel. I would also suggest shortening the log to the relevant lines and putting it in a code block (use the button above the text box) when you post there