Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [sick_khorana] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]

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  nf-core/rnaseq 3.18.0dev
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Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt
  remove_ribo_rna             : true

UMI options
  umitools_bc_pattern         : NNNN

Alignment options
  pseudo_aligner              : salmon

Process skipping options
  skip_bbsplit                : false

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

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : sick_khorana
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
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* 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: The following invalid input values have been detected:

* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/


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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[fa/8e782f] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[7c/fd7571] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[7c/b7a286] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[d4/8b2b36] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[cb/ddcec4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)` terminated with an error exit status (1)


Command executed:

  [ ! -f  WT_REP2_trimmed_1.fastq.gz ] && ln -s SRR6357072_1.fastq.gz WT_REP2_trimmed_1.fastq.gz
  [ ! -f  WT_REP2_trimmed_2.fastq.gz ] && ln -s SRR6357072_2.fastq.gz WT_REP2_trimmed_2.fastq.gz
  trim_galore \
      --fastqc_args '-t 2' \
      --cores 1 \
      --paired \
      --gzip \
      WT_REP2_trimmed_1.fastq.gz \
      WT_REP2_trimmed_2.fastq.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE":
      trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
      cutadapt: $(cutadapt --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  igzip command line interface 2.31.0

Command error:
  
  No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
  
  
  
  AUTO-DETECTING ADAPTER TYPE
  ===========================
  Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> WT_REP2_trimmed_1.fastq.gz <<)
  
  igzip: Error WT_REP2_trimmed_1.fastq.gz does not contain a complete gzip file
  Found perfect matches for the following adapter sequences:
  Adapter type	Count	Sequence	Sequences analysed	Percentage
  Illumina	296	AGATCGGAAGAGC	7635	3.88
  Nextera	0	CTGTCTCTTATA	7635	0.00
  smallRNA	0	TGGAATTCTCGG	7635	0.00
  Using Illumina adapter for trimming (count: 296). Second best hit was Nextera (count: 0)
  
  Writing report to 'WT_REP2_trimmed_1.fastq.gz_trimming_report.txt'
  
  SUMMARISING RUN PARAMETERS
  ==========================
  Input filename: WT_REP2_trimmed_1.fastq.gz
  Trimming mode: paired-end
  Trim Galore version: 0.6.10
  Cutadapt version: 4.9
  Number of cores used for trimming: 1
  Quality Phred score cutoff: 20
  Quality encoding type selected: ASCII+33
  Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
  Maximum trimming error rate: 0.1 (default)
  Minimum required adapter overlap (stringency): 1 bp
  Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
  Running FastQC on the data once trimming has completed
  Running FastQC with the following extra arguments: '-t 2'
  Output file(s) will be GZIP compressed
  
  Cutadapt seems to be fairly up-to-date (version 4.9). Setting -j 1
  Writing final adapter and quality trimmed output to WT_REP2_trimmed_1_trimmed.fq.gz
  
  
    >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file WT_REP2_trimmed_1.fastq.gz <<< 
  This is cutadapt 4.9 with Python 3.12.7
  Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC WT_REP2_trimmed_1.fastq.gz
  Processing single-end reads on 1 core ...
  Compressed file ended before the end-of-stream marker was reached
  
  
  Cutadapt terminated with exit signal: '256'.
  Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/work/7c/b7a2860dec585f4aecba6e898d7765

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/meta/nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors-
Nextflow stderr:

Nextflow 24.10.2 is available - Please consider updating your version to it