NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN_IGENOMES Segmentation fault

[fjosefdz]

Description of the bug

Hi, I am trying to run the rnaseq pipeline (3.14.0) but I always get stack in the STAR_ALIGN_IGENOMES. THerror is:

.command.sh: line 10: 42 Segmentation fault

I am using singularity in a HPC, sending the job throught slurm. I tried to add more CPUs and more RAM space but is always the same error. Is it a way to fix it? Is it a problem with the STAR version (2.7.10a)?

Command used and terminal output

source /home/conda/miniconda3/bin/activate env_nf

nextflow run nf-core/rnaseq  \
      --input /path/to/samplesheet.csv  \
      --outdir /path/to/output/  \
      --genome GRCh37  \
      --aligner 'star_salmon'  \
      -profile singularity  \
      --max_memory '64.GB'  \
      --max_cpus 16  \
      --max_time '240.h'  \
      -r 3.14.0  \

The error is similar to this one:
#684 (comment)

Relevant files

No response

System information

No response

[maxulysse]

Can you share more information, like the .nextflow.log file?

[fjosefdz]

Sure. Thank you.
.nextflow.log

[pinin4fjords]

Do you also have the STAR logs from the process directory?

Also, just to be clear, something like --max_memory '64.GB' sets the maximum bounds on memory for the workflow as a whole, and in the case of STAR this would be a reduction of the default memory allocation.

[fjosefdz]

Do you mean this?

path/to/test/test_output/nextflow_work/67/8bff9d83c65cb091f7207dd3befa38/.command.sh: line 10: 44 Segmentation fault STAR --genomeDir SAindex --readFilesIn sample_test_1_val_1.fq.gz sample_test_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix e_pal_1001_11_c_1_r. --sjdbGTFfile genome.filtered.gtf --outSAMattrRGline ID:e_pal_1001_11_c_1_r 'SM:e_pal_1001_11_c_1_r' --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif

I also tried running using --aligner 'star_rsem' and it works. Is it star_rsem using another version of STAR? How could be run with rsem but not with salmon?

[fjosefdz]

This is the code I use for running the nfcore rnaseq pipeline throught slurm:

#!/bin/bash
#SBATCH --job-name=nfcore_rnaseq
#SBATCH --partition cpu
#SBATCH --nodes 1
#SBATCH --tasks-per-node 2
#SBATCH --cpus-per-task 24
#SBATCH --time 24:00:00
#SBATCH --mem 128G
#SBATCH --output /home/isilon/onko_datasets/test/%x_%j.out
#SBATCH --error /home/isilon/onko_datasets/test/%x_%j.err

source path/to/conda/miniconda3/bin/activate base
conda activate path/to/.conda/envs/env_nf

export NXF_SINGULARITY_CACHEDIR=path/to/nf-core_rnaseq/nf-core_rnaseq_singularity/"

nextflow run nf-core/rnaseq
--input /path/to/samplesheet.csv
--outdir /path/to/output/
--genome GRCh37
--aligner 'star_salmon'
-profile singularity
--max_memory '64.GB'
--max_cpus 16
--max_time '240.h'
-r 3.14.0 \

[pinin4fjords]

Do you mean this?

No, if you have a look in the process work directory for STAR there should be more logs that might tell us where it's failing.