Hi everyone! The pipeline failed with the following message:

executor >  slurm (116)
[34/1b96de] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔
[c6/23457d] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔
[2e/f24243] NFC…_GETCHROMSIZES (genome.fa) | 1 of 1 ✔
[af/8bd231] NFC…ENOME:SORTMERNA_INDEX ([]) | 1 of 1 ✔
[-        ] NFC…_SETSTRANDEDNESS:CAT_FASTQ -
[b4/634dc4] NFC…RANDEDNESS:FQ_LINT (WTRPF) | 22 of 22 ✔
[57/4ef323] NFC…IMGALORE:FASTQC (WTBTOTAL) | 22 of 22 ✔
[54/0bd6c4] NFC…GALORE:TRIMGALORE (WTBRPF) | 22 of 22 ✔
[f2/36dc06] NFC…NT_AFTER_TRIMMING (WTBRPF) | 22 of 22 ✔
[49/c66e39] NFC…DNESS:SORTMERNA_INDEX ([]) | 1 of 1 ✔
[f9/caf96d] NFC…DNESS:SORTMERNA (33661RPF) | 20 of 24, failed: 5, retries: 2
[-        ] NFC…SS:FQ_LINT_AFTER_SORTMERNA -
[-        ] NFC…PLE_FQ_SALMON:SALMON_INDEX -
[-        ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE -
[-        ] NFC…PLE_FQ_SALMON:SALMON_QUANT -
[-        ] NFC…ASTQ_ALIGN_STAR:STAR_ALIGN -
[-        ] NFC…TOOLS_GENOME:SAMTOOLS_SORT -
[-        ] NFC…OOLS_GENOME:SAMTOOLS_INDEX -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[-        ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[bd/fe31b4] NFC…OTRICER_PREPAREORFS (null) | 1 of 1 ✔
Plus 18 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (13_85TOTAL_RNA)'

Caused by:
  Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (13_85TOTAL_RNA)` terminated for an unknown reason -- Likely it has been terminated by the external system


Command executed:

  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 13_85TOTAL_RNA_1_val_1.fq.gz --reads 13_85TOTAL_RNA_2_val_2.fq.gz \
      --threads 12 \
      --workdir . \
      --aligned rRNA_reads --fastx --other non_rRNA_reads \
      --paired_in \
      --out2 \
      --num_alignments 1 -v --index 0
  
  
          mv non_rRNA_reads_fwd.f*q.gz 13_85TOTAL_RNA_1.non_rRNA.fastq.gz
          mv non_rRNA_reads_rev.f*q.gz 13_85TOTAL_RNA_2.non_rRNA.fastq.gz
          mv rRNA_reads.log 13_85TOTAL_RNA.sortmerna.log
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA":
      sortmerna: $(echo $(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  Found flag: --num_alignments
  Found value: 1 of previous flag: --num_alignments
  Found flag: -v
  Previous flag: -v is Boolean. Setting to True
  Found flag: --index
  Found value: 0 of previous flag: --index
  [opt_workdir:995] Using WORKDIR: "." as specified
  [process:1483] Processing option: aligned with value: rRNA_reads
  [process:1483] Processing option: fastx with value: 
  [process:1483] Processing option: index with value: 0
  [opt_index:1182] using 'index' with specified value 0
  [process:1483] Processing option: num_alignments with value: 1
  [process:1483] Processing option: other with value: non_rRNA_reads
  [process:1483] Processing option: out2 with value: 
  [process:1483] Processing option: paired_in with value: 
  [process:1483] Processing option: reads with value: 13_85TOTAL_RNA_1_val_1.fq.gz
  [opt_reads:98] Processing reads file [1] out of total [2] files
  [process:1483] Processing option: reads with value: 13_85TOTAL_RNA_2_val_2.fq.gz
  [opt_reads:98] Processing reads file [2] out of total [2] files
  [process:1483] Processing option: ref with value: rfam-5.8s-database-id98.fasta
  [opt_ref:158] Processing reference [1] out of total [8] references
  [opt_ref:206] File "rfam-5.8s-database-id98.fasta" exists and is readable
  [process:1483] Processing option: ref with value: rfam-5s-database-id98.fasta
  [opt_ref:158] Processing reference [2] out of total [8] references
  [opt_ref:206] File "rfam-5s-database-id98.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-arc-16s-id95.fasta
  [opt_ref:158] Processing reference [3] out of total [8] references
  [opt_ref:206] File "silva-arc-16s-id95.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-arc-23s-id98.fasta
  [opt_ref:158] Processing reference [4] out of total [8] references
  [opt_ref:206] File "silva-arc-23s-id98.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-bac-16s-id90.fasta
  [opt_ref:158] Processing reference [5] out of total [8] references
  [opt_ref:206] File "silva-bac-16s-id90.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-bac-23s-id98.fasta
  [opt_ref:158] Processing reference [6] out of total [8] references
  [opt_ref:206] File "silva-bac-23s-id98.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-euk-18s-id95.fasta
  [opt_ref:158] Processing reference [7] out of total [8] references
  [opt_ref:206] File "silva-euk-18s-id95.fasta" exists and is readable
  [process:1483] Processing option: ref with value: silva-euk-28s-id98.fasta
  [opt_ref:158] Processing reference [8] out of total [8] references
  [opt_ref:206] File "silva-euk-28s-id98.fasta" exists and is readable
  [process:1483] Processing option: threads with value: 12
  [process:1483] Processing option: v with value: 
  [process:1503] === Options processing done ===
  [process:1504] Alignment type: [best:1 num_alignments:1 min_lis:2 seeds:2]
  [validate_kvdbdir:1248] Key-value DB location "./kvdb"
  [validate_kvdbdir:1284] Creating KVDB directory: "./kvdb"
  [validate_idxdir:1214] Using index directory: "/gpfs/commons/home/rmassoni/cll_btk_resistance/current/CLLU1/work/9e/79488f8f8f0ebb4d2d969a8487abe6

Command error:
  INFO:    Mounting image with FUSE.

Work dir:
  /gpfs/commons/home/rmassoni/cll_btk_resistance/current/CLLU1/work/9e/79488f8f8f0ebb4d2d969a8487abe6

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

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

I tried searching the error but nothing clear came out. Could you please help me troubleshoot it? Thanks!

This message:

Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (13_85TOTAL_RNA)` terminated for an unknown reason -- Likely it has been terminated by the external system

... suggests an issue native to your local infrastructure. You'd need to work out why that node killed the job

thanks Jonathan