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process hisat2-align-s runs for several days using a single thread until time limit is reached #1075

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mplescher opened this issue Sep 19, 2023 · 3 comments
Closed

process hisat2-align-s runs for several days using a single thread until time limit is reached #1075

mplescher opened this issue Sep 19, 2023 · 3 comments
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bug Something isn't working

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@mplescher
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mplescher commented Sep 19, 2023 •
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Description of the bug

I am running the rnaseq pipeline on a human data set. The process terminates with an exceeded time limit error for the HISAT2_ALIGN task. I have already increased the time limit from 16h to 48h - same result.

htop reveals a command that is running on a single thread for several days:

/home/rnaseq-analyzer/work/conda/env-d4723afd02e1ef7f40bf4372a6824844/bin/hisat2-align-s --wrapper basic-0 -x ./hisat2-index/Homo_sapiens.GRCh38.dna_sm.primary_assembly --known-splicesite-infile Homo_sapiens.GRCh38.110.splice_sites.txt --summary-file HUMAN.hisat2.summary.log --threads 12 --rg-id HUMAN --rg SM:HUMAN --met-stderr --new-summary --dta --read-lengths 72,71,70,69,67,68,47,66,57,65,64,46,45,63,61,59,58,56,55,52,51,43,42,37,25,23 -U /tmp/18514.unp

Am I doing something wrong here? We would like to use this pipeline for medical research, but a runtime of several days using only a single thread is unacceptable. I would be very grateful for any help.

Command used and terminal output

nextflow run nf-core-rnaseq/3_12_0/main.nf -profile med5 -params-file params.yaml --skip_stringtie

The process terminates with an exceeded time limit error for the HISAT2_ALIGN task.
I am working on reproducing the terminal output..

Relevant files

samplesheet.csv
params_yaml.txt
med5_config.txt
(config and yaml file upload is not supported, so I provide these files as txt here)

download reference genome data:

VERSION=110
wget -qL ftp://ftp.ensembl.org/pub/release-$VERSION/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
wget -qL ftp://ftp.ensembl.org/pub/release-$VERSION/gtf/homo_sapiens/Homo_sapiens.GRCh38.$VERSION.gtf.gz

The files Homo_sapiens.GRCh38.110.splice_sites.txt and genome.transcripts.fa as well as the index files for hisat2 and salmon were created by the pipeline itself and saved for further usage (via --save_reference).

The input data_001.fastq.gz has a size of 1,4 GB.

System information

nf-core/rnaseq 3.12.0
nextflow 23.04.3
conda 23.7.3

ubuntu 22.04
(local execution)
@mplescher mplescher added the bug Something isn't working label Sep 19, 2023
@mplescher
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mplescher commented Sep 19, 2023 •
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You may need to use --skip_stringtie in order to prevent #1074 .

@mplescher
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I run the process with a time limit of 10h for the HISAT2_ALIGN task. (It shows similar behavior for 16h and 48h.)
I can't watch htop all the time, but when I take a look after a couple of hours or the next day, it seems to use a single thread (although it should use 12 threads).

Terminal output:

nextflow run nf-core-rnaseq/3_12_0/main.nf -profile med5 -params-file params.yaml
N E X T F L O W  ~  version 23.04.3
Launching `nf-core-rnaseq/3_12_0/main.nf` [kickass_goldstine] DSL2 - revision: f421ddc35d


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.12.0
------------------------------------------------------
Core Nextflow options
  runName               : kickass_goldstine
  launchDir             : /home/rnaseq-analyzer
  workDir               : /home/rnaseq-analyzer/work
  projectDir            : /home/rnaseq-analyzer/nf-core-rnaseq/3_12_0
  userName              : rnaseq-analyzer
  profile               : med5
  configFiles           : /home/rnaseq-analyzer/nf-core-rnaseq/3_12_0/nextflow.config

Input/output options
  input                 : data/samplesheet.csv
  outdir                : output_files/

UMI options
  skip_umi_extract      : true

Read filtering options
  remove_ribo_rna       : true
  ribo_database_manifest: data/rrna-db.txt

Reference genome options
  fasta                 : data/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
  gtf                   : data/Homo_sapiens.GRCh38.110.gtf
  transcript_fasta      : data/genome.transcripts.fa
  splicesites           : data/Homo_sapiens.GRCh38.110.splice_sites.txt
  hisat2_index          : data/hisat2-index/
  salmon_index          : data/salmon-index/
  igenomes_ignore       : true

Read trimming options
  extra_trimgalore_args : --stringency 5 --trim-n --illumina

Alignment options
  aligner               : hisat2

Process skipping options
  skip_deseq2_qc        : true

Institutional config options
  custom_config_base    : /home/rnaseq-analyzer/nf-core-rnaseq/3_12_0/../configs/
  config_profile_name   : med5

Max job request options
  max_memory            : 14.GB

!! 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: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
executor >  local (6)
[3b/884e35] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.110.gtf)                                 [100%] 1 of 1 ✔
[95/a44570] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔
[eb/ffffee] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                                      [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                                               -
[e9/e65d21] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (HUMAN)                                      [100%] 1 of 1 ✔
[6a/101164] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (HUMAN)                                  [100%] 1 of 1 ✔
[c5/b86588] process > NFCORE_RNASEQ:RNASEQ:SORTMERNA (HUMAN)                                                                    [  0%] 0 of 1
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS      -
[-        ] 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                                                              -
executor >  local (7)
[3b/884e35] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.110.gtf)                                 [100%] 1 of 1 ✔
[95/a44570] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔
[eb/ffffee] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                                      [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                                               -
[e9/e65d21] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (HUMAN)                                      [100%] 1 of 1 ✔
[6a/101164] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (HUMAN)                                  [100%] 1 of 1 ✔
[c5/b86588] process > NFCORE_RNASEQ:RNASEQ:SORTMERNA (HUMAN)                                                                    [100%] 1 of 1 ✔
[79/c46387] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (HUMAN)                                              [  0%] 0 of 1
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS      -
[-        ] 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                                                                   -
executor >  local (7)
[3b/884e35] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.110.gtf)                                 [100%] 1 of 1 ✔
[95/a44570] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔
[eb/ffffee] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                                      [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                                               -
[e9/e65d21] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (HUMAN)                                      [100%] 1 of 1 ✔
[6a/101164] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (HUMAN)                                  [100%] 1 of 1 ✔
[c5/b86588] process > NFCORE_RNASEQ:RNASEQ:SORTMERNA (HUMAN)                                                                    [100%] 1 of 1 ✔
[79/c46387] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (HUMAN)                                              [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS      -
[-        ] 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                      -
executor >  local (7)
[3b/884e35] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.110.gtf)                                 [100%] 1 of 1 ✔
[95/a44570] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔
[eb/ffffee] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                                      [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                                               -
[e9/e65d21] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (HUMAN)                                      [100%] 1 of 1 ✔
[6a/101164] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (HUMAN)                                  [100%] 1 of 1 ✔
[c5/b86588] process > NFCORE_RNASEQ:RNASEQ:SORTMERNA (HUMAN)                                                                    [100%] 1 of 1 ✔
[79/c46387] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (HUMAN)                                              [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS      -
[-        ] 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:CUSTOM_DUMPSOFTWAREVERSIONS                                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC                                                                              -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (HUMAN)'

Caused by:
  Process exceeded running time limit (10h)

Command executed:

  INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2$//'`
  hisat2 \
      -x $INDEX \
      -U HUMAN.non_rRNA.fastq.gz \
       \
      --known-splicesite-infile Homo_sapiens.GRCh38.110.splice_sites.txt \
      --summary-file HUMAN.hisat2.summary.log \
      --threads 12 \
      --rg-id HUMAN --rg SM:HUMAN \
       \
      --met-stderr --new-summary --dta \
      | samtools view -bS -F 4 -F 256 - > HUMAN.bam
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN":
      hisat2: 2.2.1
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /home/rnaseq-analyzer/work/79/c4638765be92737bf456221cf6795b

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

nextflow.log
command_sh.txt

@mplescher
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I finally found the issue here! I created the HISAT2 index on another machine with far more memory, so splice sites and exons were used to build the HISAT2 index. For some reason this option broke the index. Building the HISAT2 index without usage of splice sites and exons and using the --known-splicesite-infile option for the alignment step works just fine.

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