nf-core/denovotranscript

Segmentation fault in TRINITY process when running from singularity image

Closed this issue · 3 comments

IdoBar commented

Description of the bug

A segmentation fault error occurred in the TRINITY process during the jellyfish stage when it was run from the Singularity image.
It seems to be similar to this reported issue and the authors recommend using their container (see their response at the bottom of the thread).
This should be corrected at the Trinity nf-core module.

Command used and terminal output

$ nextflow run nf-core/denovotranscript -r 1.0.0 --input Mnova_samplesheet.csv --transrate_reference /home/ibar/adna/sandbox/OTE14085/GIU3625_Humpback_whale.transcript.fasta --outdir assembly_results --assemblers trinity -with-tower -profile apptainer,bunya -c /home/ibar/.nextflow/bunya.config 


 The exit status of the task that caused the workflow execution to fail was: 2

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

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY (pooled_reads)` terminated with an error exit status (2)


Command executed:

  # Note that Trinity needs the word 'trinity' in the outdir
  
  Trinity \
      --seqType fq \
      --max_memory 160G \
      --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz \
      --output pooled_reads_trinity \
      --CPU 12 \
       \
      > >(tee pooled_reads.log)
  
  gzip \
      -cf \
      pooled_reads_trinity.Trinity.fasta \
      > pooled_reads.fa.gz
  
  rm pooled_reads_trinity.Trinity.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY":
      trinity: $(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
  END_VERSIONS

Command exit status:
  2

Command output:
  Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
  Sequence: GGGGTGAACTCGGCGGGis smaller than 25 base pairs, skipping
  Sequence: CTCCGTTTCCGACCTGGGCis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: ACTCCCCTCGCCGGGGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCGGGGGCGGGGAGCGGGGCGTGCis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCCTCCGTCGCCGGGis smaller than 25 base pairs, skipping
  Sequence: GGGCGGGGAGCGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: GAAGAGGGGAGGGCGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCGGGATTCGGCGAGTGCTGCTGis smaller than 25 base pairs, skipping
  Sequence: TCCCGCCGGCGGGAGCCCis smaller than 25 base pairs, skipping
  Sequence: CGGGCAGGAGGATCGCTTGAGCCis smaller than 25 base pairs, skipping
  Sequence: GTAACACTCGGGGCGis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCGGGGis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCCGGGCGis smaller than 25 base pairs, skipping
  STATS_GENERATION_TIME: 8147 seconds.
  CMD finished (9881 seconds)
  STATS_GENERATION_TIME: 9028 seconds.
  CMD finished (11528 seconds)
  CMD: touch left.fa.K25.stats.ok
  CMD finished (0 seconds)
  CMD: touch right.fa.K25.stats.ok
  CMD finished (0 seconds)
  -sorting each stats file by read name.
  CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
  CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
  bash: line 1: 140302 Broken pipe             tail -n +2 left.fa.K25.stats
       140303 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
  Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  bash: line 1: 140304 Broken pipe             tail -n +2 right.fa.K25.stats
       140305 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
  Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
  Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 160G  --max_cov 200 --min_cov 1 --CPU 12 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000  --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together  --PARALLEL_STATS   died with ret 7424 at /usr/local/bin/Trinity line 2919.
  	main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
  	main::normalize("/scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotrans"..., 200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 3412
  	main::run_normalization(200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 1450

Command wrapper:
  Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
  Sequence: GGGGTGAACTCGGCGGGis smaller than 25 base pairs, skipping
  Sequence: CTCCGTTTCCGACCTGGGCis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: ACTCCCCTCGCCGGGGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCGGGGGCGGGGAGCGGGGCGTGCis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCCTCCGTCGCCGGGis smaller than 25 base pairs, skipping
  Sequence: GGGCGGGGAGCGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: GAAGAGGGGAGGGCGGGCCGGGCis smaller than 25 base pairs, skipping
  Sequence: CCGGGATTCGGCGAGTGCTGCTGis smaller than 25 base pairs, skipping
  Sequence: TCCCGCCGGCGGGAGCCCis smaller than 25 base pairs, skipping
  Sequence: CGGGCAGGAGGATCGCTTGAGCCis smaller than 25 base pairs, skipping
  Sequence: GTAACACTCGGGGCGis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCGGGGis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCGGGGAGCCGGGCGis smaller than 25 base pairs, skipping
  Sequence: TCCGGGGGCCGGGCGis smaller than 25 base pairs, skipping
  STATS_GENERATION_TIME: 8147 seconds.
  CMD finished (9881 seconds)
  STATS_GENERATION_TIME: 9028 seconds.
  CMD finished (11528 seconds)
  CMD: touch left.fa.K25.stats.ok
  CMD finished (0 seconds)
  CMD: touch right.fa.K25.stats.ok
  CMD finished (0 seconds)
  -sorting each stats file by read name.
  CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
  CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
  bash: line 1: 140302 Broken pipe             tail -n +2 left.fa.K25.stats
       140303 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
  Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  bash: line 1: 140304 Broken pipe             tail -n +2 right.fa.K25.stats
       140305 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
  Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
  Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 160G  --max_cov 200 --min_cov 1 --CPU 12 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000  --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together  --PARALLEL_STATS   died with ret 7424 at /usr/local/bin/Trinity line 2919.
  	main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
  	main::normalize("/scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotrans"..., 200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 3412
  	main::run_normalization(200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 1450

Work dir:
  /scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotranscript_assembly/work/fc/c26cbe596b01b63a68ee82ae92682d

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Relevant files

No response

System information

  • Nextflow version (eg. 24.04.4)
  • Hardware: HPC
  • Executor: slurm
  • Container engine: Apptainer
  • OS: Rocky Linux release 8.10 (Green Obsidian)
  • Version of nf-core/denovotranscript: 1.0.0
hisoph commented

Hi we also have this same issue.

Here is my command from nf-core/denovotranscript:

nextflow run 'https://github.com/nf-core/denovotranscript'
		 -name lonely_goodall
		 -params-file 'https://api.cloud.seqera.io/ephemeral/el5qGrmnkQjDxrnJLWZdQw.json'
		 -with-tower
		 -r 1.0.0
		 -profile york_viking

Here is my error

Workflow execution completed unsuccessfully
The exit status of the task that caused the workflow execution to fail was: 2

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

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY (pooled_reads)` terminated with an error exit status (2)


Command executed:

  # Note that Trinity needs the word 'trinity' in the outdir
  
  Trinity \
      --seqType fq \
      --max_memory 400G \
      --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz \
      --output pooled_reads_trinity \
      --CPU 40 \
       \
      > >(tee pooled_reads.log)
  
  gzip \
      -cf \
      pooled_reads_trinity.Trinity.fasta \
      > pooled_reads.fa.gz
  
  rm pooled_reads_trinity.Trinity.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY":
      trinity: $(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
  END_VERSIONS

Command exit status:
  2

Command output:
  Sequence: GTCGTATCTTTGGTCTTATATTTis smaller than 25 base pairs, skipping
  Sequence: GTTGTTAACTGGGTCGGCAis smaller than 25 base pairs, skipping
  Sequence: GTTTTCAGTGCATTCGTGGGis smaller than 25 base pairs, skipping
  Sequence: GAACAAGTGTCTGTTCCis smaller than 25 base pairs, skipping
  Sequence: GCCGGAACCTCGCCGGis smaller than 25 base pairs, skipping
  Sequence: CACAGTAGTACATTTis smaller than 25 base pairs, skipping
  Sequence: ATTCCATTCCATTAAis smaller than 25 base pairs, skipping
  Sequence: CCCCTCCGCATAGCGATCGis smaller than 25 base pairs, skipping
  Sequence: GAAATATGAAAACCGTAis smaller than 25 base pairs, skipping
  Sequence: CGGCGGCGCGTGGGGGTGis smaller than 25 base pairs, skipping
  Sequence: CCCTCGCCGTTTACTAGAGCCis smaller than 25 base pairs, skipping
  Sequence: ATTCTTTTTGCACATATGGGis smaller than 25 base pairs, skipping
  Sequence: GAGAAGGGTTTTGTGTGis smaller than 25 base pairs, skipping
  Sequence: ATTTTCTCCCCTTGCis smaller than 25 base pairs, skipping
  Sequence: CCGATGCACGTTGCTTTGis smaller than 25 base pairs, skipping
  Sequence: GTGAGGTACTCGGGGis smaller than 25 base pairs, skipping
  Sequence: CCTGCTTCGGGGCTGTTTTis smaller than 25 base pairs, skipping
  Sequence: CTTAGCATGCCATTTTTTACis smaller than 25 base pairs, skipping
  Sequence: GTTTTAATAGAATGATCis smaller than 25 base pairs, skipping
  Sequence: CCGGGATTCTAGTTACTis smaller than 25 base pairs, skipping
  Sequence: GCACGTTTGATACAGis smaller than 25 base pairs, skipping
  Sequence: TCTGTATGTGCGCTGGTACis smaller than 25 base pairs, skipping
  Sequence: CTTTCCACTTTCTGGAis smaller than 25 base pairs, skipping
  Sequence: TGGGGAATGCCGAGGis smaller than 25 base pairs, skipping
  Sequence: GCCTTACTGTGTGCGis smaller than 25 base pairs, skipping
  Sequence: GCTTCACAATATCCCACCCis smaller than 25 base pairs, skipping
  STATS_GENERATION_TIME: 13462 seconds.
  CMD finished (15805 seconds)
  CMD: touch left.fa.K25.stats.ok
  CMD finished (0 seconds)
  CMD: touch right.fa.K25.stats.ok
  CMD finished (0 seconds)
  -sorting each stats file by read name.
  CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort
  CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort
  bash: line 1: 212644 Broken pipe             tail -n +2 right.fa.K25.stats
       212645 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort
  Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  bash: line 1: 212646 Broken pipe             tail -n +2 left.fa.K25.stats
       212647 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort
  Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
  Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 200G  --max_cov 200 --min_cov 1 --CPU 40 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000  --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together  --PARALLEL_STATS   died with ret 7424 at /usr/local/bin/Trinity line 2919.
  	main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
  	main::normalize("/mnt/scratch/projects/biol-tf-2018/nextflow/work/89/d975ba4cc"..., 200, ARRAY(0x5555558ddcf8), ARRAY(0x55555593dfc0)) called at /usr/local/bin/Trinity line 3412
  	main::run_normalization(200, ARRAY(0x5555558ddcf8), ARRAY(0x55555593dfc0)) called at /usr/local/bin/Trinity line 1450

Command wrapper:
  Sequence: GCACGTTTGATACAGis smaller than 25 base pairs, skipping
  Sequence: TCTGTATGTGCGCTGGTACis smaller than 25 base pairs, skipping
  Sequence: CTTTCCACTTTCTGGAis smaller than 25 base pairs, skipping
  Sequence: TGGGGAATGCCGAGGis smaller than 25 base pairs, skipping
  Sequence: GCCTTACTGTGTGCGis smaller than 25 base pairs, skipping
  Sequence: GCTTCACAATATCCCACCCis smaller than 25 base pairs, skipping
  STATS_GENERATION_TIME: 13462 seconds.
  CMD finished (15805 seconds)
  CMD: touch left.fa.K25.stats.ok
  CMD finished (0 seconds)
  CMD: touch right.fa.K25.stats.ok
  CMD finished (0 seconds)
  -sorting each stats file by read name.
  CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort
  CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort
  bash: line 1: 212644 Broken pipe             tail -n +2 right.fa.K25.stats
       212645 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort
  Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  bash: line 1: 212646 Broken pipe             tail -n +2 left.fa.K25.stats
       212647 Segmentation fault      (core dumped) | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort
  Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 100G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
  
  Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
  Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 200G  --max_cov 200 --min_cov 1 --CPU 40 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000  --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together  --PARALLEL_STATS   died with ret 7424 at /usr/local/bin/Trinity line 2919.
  	main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
  	main::normalize("/mnt/scratch/projects/biol-tf-2018/nextflow/work/89/d975ba4cc"..., 200, ARRAY(0x5555558ddcf8), ARRAY(0x55555593dfc0)) called at /usr/local/bin/Trinity line 3412
  	main::run_normalization(200, ARRAY(0x5555558ddcf8), ARRAY(0x55555593dfc0)) called at /usr/local/bin/Trinity line 1450
  
  ============================
   Job utilisation efficiency
  ============================
  
  Job ID: 12323098
  Cluster: alces.network
  User/Group: clusterusers
  State: FAILED (exit code 2)
  Nodes: 1
  Cores per node: 40
  CPU Utilized: 2-19:59:36
  CPU Efficiency: 25.04% of 11-07:34:00 core-walltime
  Job Wall-clock time: 06:47:21
  Memory Utilized: 89.94 GB
  Memory Efficiency: 17.99% of 500.00 GB
   Requested wall clock time: 2-00:00:00
      Actual wall clock time: 06:47:21
  Wall clock time efficiency: 14.1%
             Job queued time: 00:00:32
avani-bhojwani commented

It seems to be related to the container not having the dependency required to use the sort command. I have updated the container. I will update the pipeline to use the new container.

avani-bhojwani commented

The update has gone through.

l also increased the amount of resources allocated for Trinity in the latest release. However, if you still run out of time/memory/etc, please let me know the size of your datasets (number of samples and number of reads/sample) or an estimation of resources you would like to have for this step.

Thanks!

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