Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 250.

The full error message was:

Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)'

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)` terminated with an error exit status (250)


Command executed:

  spades.py \
      --rna \
      --threads 12 \
      --memory 72 \
       \
      -1 pooled_reads_1.merged.fastq.gz -2 pooled_reads_2.merged.fastq.gz   \
       \
      -o ./
  mv spades.log pooled_reads.spades.log
  
  if [ -f scaffolds.fasta ]; then
      mv scaffolds.fasta pooled_reads.scaffolds.fa
      gzip -n pooled_reads.scaffolds.fa
  fi
  if [ -f contigs.fasta ]; then
      mv contigs.fasta pooled_reads.contigs.fa
      gzip -n pooled_reads.contigs.fa
  fi
  if [ -f transcripts.fasta ]; then
      mv transcripts.fasta pooled_reads.transcripts.fa
      gzip -n pooled_reads.transcripts.fa
  fi
  if [ -f soft_filtered_transcripts.fasta ]; then
      mv soft_filtered_transcripts.fasta pooled_reads.soft_filtered_transcripts.fa
      gzip -n pooled_reads.soft_filtered_transcripts.fa
  fi
  if [ -f hard_filtered_transcripts.fasta ]; then
      mv hard_filtered_transcripts.fasta pooled_reads.hard_filtered_transcripts.fa
      gzip -n pooled_reads.hard_filtered_transcripts.fa
  fi
  if [ -f assembly_graph_with_scaffolds.gfa ]; then
      mv assembly_graph_with_scaffolds.gfa pooled_reads.assembly.gfa
      gzip -n pooled_reads.assembly.gfa
  fi
  
  if [ -f gene_clusters.fasta ]; then
      mv gene_clusters.fasta pooled_reads.gene_clusters.fa
      gzip -n pooled_reads.gene_clusters.fa
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES":
      spades: $(spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p')
  END_VERSIONS

Command exit status:
  250

Command output:
    2:58:16.891    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
    2:58:16.954    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
    2:58:29.318    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
    2:58:29.382    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
    2:58:29.443    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
    2:58:29.507    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
    2:58:29.568    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
    2:58:29.631    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
    2:58:29.690    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
    2:58:29.750    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
    2:58:29.809    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
    2:58:29.869    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running AT Tips
    2:58:29.928    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   AT Tips triggered 0 times
    2:58:29.987    49G / 57G   INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
    2:58:32.102    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
    2:58:35.568    49G / 57G   INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 2140990 times
    2:58:36.049    49G / 57G   INFO    General                 (simplification.cpp        : 508)   After simplification:
    2:58:36.110    49G / 57G   INFO    General                 (simplification.cpp        : 509)     Average coverage = 194.651
    2:58:36.669    49G / 57G   INFO    General                 (simplification.cpp        : 510)     Total length = 202779300
    2:58:37.195    49G / 57G   INFO    General                 (simplification.cpp        : 511)     Median edge length: 356
    2:58:37.261    49G / 57G   INFO    General                 (simplification.cpp        : 512)     Edges: 2070079
    2:58:37.321    49G / 57G   INFO    General                 (simplification.cpp        : 513)     Vertices: 2424436
    2:58:37.382    49G / 57G   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Mismatch Correction (id: mismatch_correction)
    2:58:37.442    49G / 57G   INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
    2:58:37.502    49G / 57G   INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 225479915)
    2:58:39.137    49G / 57G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
    2:58:56.297    49G / 57G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 202779278 kmers, 146680906 bytes occupied (5.78682 bits per kmer).
    2:58:56.916    50G / 57G   INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
    2:59:04.393    50G / 57G   INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 662334904 kmers to process
  mimalloc: error: unable to allocate OS memory (5305794560 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)
  mimalloc: process info:
     elapsed:   10841.233 s
     process: user: 94959.883 s, system: 1410.633 s, faults: 351352
         rss: current: 126547222528, peak: 70665609216
      commit: current: 126547222528, peak: 126547222528
  
  
  == Error ==  system call for: "['/usr/local/bin/spades-core', '/gscratch/scrubbed/srlab/nxf.si5WitkIa9/K43/configs/config.info', '/gscratch/scrubbed/srlab/nxf.si5WitkIa9/K43/configs/mda_mode.info', '/gscratch/scrubbed/srlab/nxf.si5WitkIa9/K43/configs/rna_mode.info']" finished abnormally, OS return value: -6
  None
  
  In case you have troubles running SPAdes, you can report an issue on our GitHub repository github.com/ablab/spades
  Please provide us with params.txt and spades.log files from the output directory.
  
  SPAdes log can be found here: /gscratch/scrubbed/srlab/nxf.si5WitkIa9/spades.log
  
  Thank you for using rnaSPAdes! If you use it in your research, please cite:
  
    Bushmanova, E., Antipov, D., Lapidus, A. and Prjibelski, A.D., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience, 8(9), p.giz100.
    doi.org/10.1093/gigascience/giz100

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  /usr/local/share/spades/spades_pipeline/support.py:488: SyntaxWarning: invalid escape sequence '\d'
    return [atoi(c) for c in re.split("(\d+)", text)]

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20241104_denovo/work/45/138d60fae9524f20eb79462e1b8d06

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