Salmon quant error in --ont mode (Bus error (core dumped)

[rugilemat]

Hi,

I have been trying to run the installed salmon version on our HPC cluster on minimap aligned ONT reads and got the following error:

processed 0 reads in current round/var/lib/slurm/slurmd/job10333001/slurm_script: line 25: 2153273 Bus error (core dumped)

My script was as follows:

module load salmon/1.9.0-gcc-10.3.0
cd /scratch/prj/ppn_microglia_mod/targeted/transcriptome/clean/transcriptome

for bc in {01..54}; do

salmon quant  --ont -t /scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa -l A -a "combined_BC"$bc"_aligned.bam" -o "BC"$bc"_transcripts_quant"

done

Salmon version was 1.9.0
Transcriptome ref: Homo Sapiens Gencode v.44

The directories were generated for the barcodes and contain aux info, cmd_info.json, libParams and logs but the directories/files are empty.

The command was run through slurm scheduler on HPC cluster.

The output log looks like (repeated for for loop):

Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
Sign up for the salmon mailing list to hear about new versions, features and updates at:
https://oceangenomics.com/subscribe
# salmon (alignment-based) v1.9.0
# [ program ] => salmon 
# [ command ] => quant 
# [ ont ] => { }
# [ targets ] => { /scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa }
# [ libType ] => { A }
# [ alignments ] => { combined_BC01_aligned.bam }
# [ output ] => { BC01_trascripts_quant }
Logs will be written to BC01_trascripts_quant/logs
[2023-11-04 16:49:44.093] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-11-04 16:49:44.093] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
Library format { type:single end, relative orientation:none, strandedness:unstranded }
[2023-11-04 16:49:44.699] [jointLog] [info] numQuantThreads = 4
parseThreads = 4
Checking that provided alignment files have consistent headers . . . done
Populating targets from aln = "combined_BC01_aligned.bam", fasta = "/scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa" . . .done




processed 0 reads in current round/var/lib/slurm/slurmd/job10333001/slurm_script: line 25: 2152693 Bus error               (core dumped)

Any advice on this would be highly appreciated!