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GUNZIP does not work for relative paths specified with --fasta and --gtf #1311

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fbnrst opened this issue May 31, 2024 · 1 comment
Closed

GUNZIP does not work for relative paths specified with --fasta and --gtf #1311

fbnrst opened this issue May 31, 2024 · 1 comment
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bug Something isn't working Ready for review

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@fbnrst
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fbnrst commented May 31, 2024

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

$ 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 24.04.2

Launching `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                    : output

Reference 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.gz

Read filtering options
  bbsplit_fasta_list        : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt

UMI options
  umitools_bc_pattern       : NNNN

Alignment options
  pseudo_aligner            : salmon
  min_mapped_reads          : 5

Process skipping options
  skip_bbsplit              : false

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max 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.md

WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  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

Relevant files

nextflow.log

System information

  • Nextflow 24.04.2
  • HPC
  • local executor
  • CentOS Linux release 7.4.1708
  • nf-core/rnaseq v3.14.0
@fbnrst fbnrst added the bug Something isn't working label May 31, 2024
@pinin4fjords pinin4fjords mentioned this issue May 31, 2024
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@pinin4fjords
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Thanks for the report. This due the file getting passes as a string incorrectly- fixed by the PR above.

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