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unzipping of fasta and gtf files fail, when I provide a relative path to those files. I can work around by either unzipping the file first, or by providing an absolute path. Below, I provide a minimal example for just the gtf file, I get the same kind of error for the fasta file.
Command used and terminal output
$ wget https://ftp.ensembl.org/pub/release-111/gtf/mus_musculus/Mus_musculus.GRCm39.111.gtf.gz
$ nextflow run nf-core/rnaseq -profile test -r 3.14.0 --outdir output --gtf Mus_musculus.GRCm39.111.gtf.gz N E X T F L O W ~ version 24.04.2Launching `https://github.com/nf-core/rnaseq` [tiny_engelbart] DSL2 - revision: b89fac3265 [3.14.0]------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/rnaseq v3.14.0-gb89fac3------------------------------------------------------Core Nextflow options revision : 3.14.0 runName : tiny_engelbart launchDir : /lustre/projects/Fabian_Rost/temp/rnaseq workDir : /lustre/projects/Fabian_Rost/temp/rnaseq/work projectDir : /home/rost/.nextflow/assets/nf-core/rnaseq userName : rost profile : test configFiles :Input/output options input : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv outdir : outputReference genome options fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta gtf : Mus_musculus.GRCm39.111.gtf.gz gff : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz transcript_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta additional_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz hisat2_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz rsem_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz salmon_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gzRead filtering options bbsplit_fasta_list : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txtUMI options umitools_bc_pattern : NNNNAlignment options pseudo_aligner : salmon min_mapped_reads : 5Process skipping options skip_bbsplit : falseInstitutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline functionMax job request options max_cpus : 2 max_memory : 6.GB max_time : 6.h!! Only displaying parameters that differ from the pipeline defaults !!------------------------------------------------------If you use nf-core/rnaseq for your analysis please cite:* The pipeline https://doi.org/10.5281/zenodo.1400710* The nf-core framework https://doi.org/10.1038/s41587-020-0439-x* Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.mdWARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Both '--gtf' and '--gff' parameters have been provided. Using GTF file as priority.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ '--transcript_fasta' parameter has been provided. Make sure transcript names in this file match those in the GFF/GTF file. Please see: https://github.com/nf-core/rnaseq/issues/753~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX -[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX -[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA [ 0%] 0 of 1[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX [ 0%] 0 of 1[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ [ 0%] 0 of 1[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC [ 0%] 0 of 2[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA [ 0%] 0 of 1[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE -[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX [ 0%] 0 of 1[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ [ 0%] 0 of 2[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC [ 0%] 0 of 2[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE [ 0%] 0 of 2[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT -[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE -[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT -[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -[- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE -[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS -[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE -[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV -[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP -[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG -[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP -[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG -[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ -[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION -[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION -[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT -Plus 9 more processes waiting for tasks…Execution cancelled -- Finishing pending tasks before exit-[nf-core/rnaseq] Pipeline completed with errors-ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF'Caused by: Not a valid path value: 'Mus_musculus.GRCm39.111.gtf.gz'Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details
Description of the bug
unzipping of fasta and gtf files fail, when I provide a relative path to those files. I can work around by either unzipping the file first, or by providing an absolute path. Below, I provide a minimal example for just the gtf file, I get the same kind of error for the fasta file.
Command used and terminal output
Relevant files
nextflow.log
System information
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