Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: -1.

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 (-1)


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:
  -1

Command output:
    0:27:19.787  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 147845225 kmers
    0:27:22.169  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 157965512 kmers
    0:27:23.233  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 167836508 kmers
    0:27:24.539  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 182946012 kmers
    0:27:37.931  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 271475817 kmers
    0:28:12.895  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 540371395 kmers
    0:29:30.902  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 197)   Processed 1081874329 kmers
    0:31:06.702  6841M / 16G   INFO    General                 (kmer_splitters.hpp        : 202)   Used 1741249467 kmers.
    0:31:06.703     1M / 16G   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
    0:32:16.666     1M / 16G   INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 1730543626 kmers in total.
    0:32:16.666     1M / 16G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
    0:33:57.360  1217M / 16G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1730543626 kmers, 1249997920 bytes occupied (5.77852 bits per kmer).
    0:33:57.360  1217M / 16G   INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1736441856 bytes, address: 0x14f5dd989000, alignment: 67108864, commit: 1)
    0:34:23.302  2869M / 16G   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
    0:36:20.954  2869M / 16G   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
    0:36:21.053  2869M / 16G   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early A/T remover (id: construction:early_at_remover)
    0:36:21.053  2869M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 177)   Remove short poly A/T edges
    0:38:08.513  2869M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 255)   Links removed: 624
    0:38:08.513  2869M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 180)   534 44-mers were removed by early poly A/T remover
    0:38:08.624  2869M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 263)   Remove poly A/T tips
    0:39:51.399  2899M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 332)   Clipped tips: 340717
    0:39:51.399  2869M / 16G   INFO   Early A/T remover        (early_simplification.hpp  : 266)   1901281 44-mers were removed by early poly A/T tip clipper
    0:39:51.481  2869M / 16G   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
    0:39:51.484  2869M / 16G   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1799356416 bytes, address: 0x14f69de4f000, alignment: 67108864, commit: 1)
    0:42:42.957  8031M / 16G   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 112178865 sequences extracted
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1799356416 bytes, address: 0x14f570c00000, alignment: 67108864, commit: 1)
    0:44:04.967  8031M / 16G   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
    0:44:54.053  8032M / 16G   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 196 loops collected
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (3594518528 bytes, address: 0x14f6b0aff000, alignment: 67108864, commit: 1)
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1799356416 bytes, address: 0x14f644c00000, alignment: 67108864, commit: 1)
    0:44:58.793  8031M / 16G   INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
    0:45:07.113  8031M / 16G   INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
    0:45:07.113  8031M / 16G   INFO    General                 (debruijn_graph_constructor: 516)   Total 224358122 edges to create
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (9026142208 bytes, address: 0x14f356000000, alignment: 67108864, commit: 1)
    0:45:07.119    17G / 17G   INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (3594518528 bytes, address: 0x14f6b0aff000, alignment: 67108864, commit: 1)
    0:46:44.968    20G / 22G   INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
    0:46:54.003    20G / 23G   INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1077936128 bytes, address: 0x14f66fc00000, alignment: 67108864, commit: 1)
    0:46:55.978    21G / 23G   INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
    0:47:04.758    21G / 23G   INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
    0:47:04.758    21G / 23G   INFO    General                 (debruijn_graph_constructor: 542)   Total 101484665 vertices to create
    0:47:04.763    30G / 30G   INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
    0:49:06.916    24G / 27G   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
    0:49:06.917    24G / 27G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
    0:51:40.107    26G / 27G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1741238247 kmers, 1257723248 bytes occupied (5.77852 bits per kmer).
  mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (6970933248 bytes, address: 0x14ef6c800000, alignment: 67108864, commit: 1)
    0:51:46.177    32G / 32G   INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.

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/63/255e0574cfc25ee30ab75bbc073198

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