sortmerna "41 Illegal instruction"

[sunta3iouxos]

Description of the bug

Every time I am including the option to remove reads with sortmeRNA using the following settings:

{
    "input": "\/home\/tgeorgom\/nextflow\/samplesheet.csv",
    "outdir": "\/scratch\/tgeorgom\/Debarati24R9_star",
    "multiqc_title": "Debarati24R9_STAR",
    "fasta": "\/scratch\/tgeorgom\/assemblies\/GRCm39\/GRCm39.primary_assembly.genome.fa",
    "gtf": "\/scratch\/tgeorgom\/assemblies\/GRCm39\/gencode.vM36.basic.annotation.gtf",
    "transcript_fasta": "\/scratch\/tgeorgom\/assemblies\/GRCm39\/gencode.vM36.transcripts.fa",
    "rsem_index": "\/scratch\/tgeorgom\/Debarati24R9\/genome\/index\/rsem\/",
    "salmon_index": "\/scratch\/tgeorgom\/Debarati24R9\/genome\/index\/salmon\/",
    "gencode": true,
    "trimmer": "fastp",
    "extra_fastp_args": "--trim_poly_g --trim_poly_x -Q -L --correction",
    "remove_ribo_rna": true,
    "ribo_database_manifest": "\/scratch\/tgeorgom\/assemblies\/GRCm39\/sortmeRNA\/rrna-db-defaults.txt",
    "aligner": "star_salmon",
    "pseudo_aligner": "salmon",
    "seq_center": "CCG_University_of_Cologne",
    "save_non_ribo_reads": true,
    "save_reference": true,
    "save_trimmed": true,
    "save_align_intermeds": true,
    "rseqc_modules": "bam_stat, inner_distance, infer_experiment, junction_annotation, junction_saturation, read_distribution, read_duplication, tin",
    "skip_umi_extract": true,
    "skip_pseudo_alignment": true
}

The command fails with 132 exit code without any other information.

If I run locally the same command n my PC, by installing the "SortMeRNA version 4.3.7" using the same command line it goes through without any error.

 sortmerna --ref smr_v4.3_default_db.fasta --threads 16 --workdir . --index 1
[process:1393] === Options processing starts ... ===
Found value: sortmerna
Found flag: --ref
Found value: smr_v4.3_default_db.fasta of previous flag: --ref
Found flag: --threads
Found value: 16 of previous flag: --threads
Found flag: --workdir
Found value: . of previous flag: --workdir
Found flag: --index
Found value: 1 of previous flag: --index
Missing required flag: reads
[opt_workdir:995] Using WORKDIR: "/home/tgeorgom/." as specified
[process:1483] Processing option: index with value: 1
[opt_index:1182] using 'index' with specified value 1
[process:1483] Processing option: ref with value: smr_v4.3_default_db.fasta
[opt_ref:158] Processing reference [1] out of total [1] references
[opt_ref:206] File "/home/tgeorgom/smr_v4.3_default_db.fasta" exists and is readable
[process:1483] Processing option: threads with value: 16
[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 "/home/tgeorgom/./kvdb"
[validate_kvdbdir:1284] Creating KVDB directory: "/home/tgeorgom/./kvdb"
[validate_idxdir:1214] Using index directory: "/home/tgeorgom/./idx"
[validate_idxdir:1222] Created index directory - OK
[validate_readb_dir:1306] Using split reads directory : "/home/tgeorgom/./readb"
[validate_readb_dir:1314] Created split reads directory - OK
[validate_aligned_pfx:1335] Checking output directory: "/home/tgeorgom/./out"
[validate:1533] No output format has been chosen (fastx|sam|blast|otu_map). Using default 'blast'
[main:62] Running command:
sortmerna --ref smr_v4.3_default_db.fasta --threads 16 --workdir . --index 1
[build_index:1123] ==== Index building started ====
[build_index:1180] Begin indexing file smr_v4.3_default_db.fasta of size: 146741693 under index name ./idx/4383911207881337579
  done.

[build_index:2091] ==== Done index building in 555.435 sec ====

[main:72] Only performed indexing as 'index' = 1 was specified
(sortmerna) tgeorgom@DESKTOP-G1QP64E:~$ ls ./idx/
4383911207881337579.bursttrie_0.dat  4383911207881337579.kmer_0.dat  4383911207881337579.pos_0.dat  4383911207881337579.stats

Command used and terminal output

$nextflow run -c custom.config nf-core/rnaseq -profile singularity -work-dir temp/ -params-file nf-params_NewnoKrak.json -resume -bg

WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_TASK_WORKDIR as environment variable will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
/scratch/tgeorgom_temp/43/cdbc0520314ad64702234f3cfd1812/.command.sh: line 5:    41 Illegal instruction     (core dumped) sortmerna --ref smr_v4.3_default_db.fasta --threads 24 --workdir . --index 1

Relevant files

.nextflow.log

System information

Nextflow version 24.10.0.5928
Hardware: HPC
Executor: slur,
Container engine: Singularity
OS CentOS Linux
Version of  nf-core/rnaseq 3.17.0nec

[pinin4fjords]

SortMeRNA sometimes produces cryptic errors when the underlying issue is lack of memory. I'd suggest testing with as much memory as you can, and reducing from there if it works.