sortMeRNA fails

[ulbivin]

Description of the bug

I am trying to run nf-core/riboseq on a cluster computer, but it fails on the sortMeRNA step for all samples.

Command used and terminal output

I run this nextflow command:
$ nextflow run nf-core/riboseq -profile computerome --project reg_00024 --input nf-core_riboseq_sample_sheet.csv --outdir /home/projects/reg_00024/data/RiboSeq/nf-core_riboseq_out/ --fasta /home/projects/reg_00024/data/RiboSeq/ref/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz --gtf  /home/projects/reg_00024/data/RiboSeq/ref/Homo_sapiens.GRCh38.113.gtf.gz  --save_reference -resume

This is one of the error messages from the .nextflow.log file:
Jan-09 16:39:14.631 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 51991560; id: 61; name: NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:SORTMERNA (0279_05_RiboSeq); st
atus: COMPLETED; exit: 137; error: -; workDir: /home/projects/reg_00024/data/RiboSeq/work/e1/24e9e6f1ba0dd9c49c905846f6bf53 started: 1736431257223; exited: 2025-01-09T15:39:04.322921661Z; ]
Jan-09 16:39:14.636 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:SORTMERNA (0279_05_RiboSeq); work-dir=/home/projects/reg_00024/data/RiboSeq/work/e1/24e9e6f1ba0dd9c49c905846f6bf53
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:SORTMERNA (0279_05_RiboSeq)` terminated with an error exit status (137)
Jan-09 16:39:14.638 [TaskFinalizer-6] INFO  nextflow.processor.TaskProcessor - [e1/24e9e6] NOTE: Process `NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:SORTMERNA (0279_05_RiboSeq)` terminated with an error exit
status (137) -- Execution is retried (2)

I have tried allocating 256Gb memory in the .command.run file and running this (after removing the kvdb-folder):
$ bash .command.run
But I get this similar error message:

[is_split_ready:726] found existing readfeed descriptor ./readb/readfeed
/home/projects/reg_00024/data/BAT_RiboSeq_Taylah/work/e1/24e9e6f1ba0dd9c49c905846f6bf53/.command.sh: line 11:    41 Aborted                 (core dumped) sortmerna --ref rfam-5.8s-database-id98.fasta --ref rfam-5s-database-id98.fasta --ref silva-arc-16s-id95.fasta --ref silva-arc-23s-id98.fasta --ref silva-bac-16s-id90.fasta --ref silva-bac-23s-id98.fasta --ref silva-euk-18s-id95.fasta --ref silva-euk-28s-id98.fasta --reads 0279_05_RiboSeq_trimmed.fq.gz --threads 24 --workdir . --aligned rRNA_reads --fastx --other non_rRNA_reads --num_alignments 1 -v --index 0
INFO:    Cleaning up image...

I have also tried running the sortMeRNA command directly from the .command.sh file (after loading the sortmerna/4.3.6 module):

$ sortmerna \
    --ref rfam-5.8s-database-id98.fasta --ref rfam-5s-database-id98.fasta --ref silva-arc-16s-id95.fasta --ref silva-arc-23s-id98.fasta --ref silva-bac-16s-id90.fasta --ref silva-bac-23s-id98.fasta --ref silva-euk-18s-id95.fasta --ref silva-euk-28s-id98.fasta \
     \
    --reads 0279_05_RiboSeq_trimmed.fq.gz \
    --threads 24 \
    --workdir . \
    --aligned rRNA_reads --fastx --other non_rRNA_reads \
     \
     \
    --num_alignments 1 -v --index 0

This gives me this error message:

[is_split_ready:726] found existing readfeed descriptor ./readb/readfeed
terminate called after throwing an instance of 'std::out_of_range'
  what():  stoi
Aborted (core dumped)

This seems to be similar to the sortMeRNA bug described here:
https://github.com/sortmerna/sortmerna/issues/379

Can you please advice on how to preceed and if the sortMeRNA issue in the link is relevant/how to implement the solution?

I am fairly new to NextFlow, so please let me know of what info might be missing.

Relevant files

No response

System information

Nextflow version: 24.10.3
Hardware: HPC
Executor: TORQUE
Container engine: Singularity
OS: CentOS Linux release 7.6.1810
Version of nf-core/riboseq: 1.0.1