Closed
Description
Description of the bug
I have tried running the pipeline with both bwa and bwamem, either way everything seems to run fine up until the samtools sort step, which does appear to complete on the first sample, but not the second sample regardless of which sample is second. I have tried running samtools sort on the bams created by the pipeline independently and it works just fine for all of my samples when I run it. The error message I am given from the pipeline is: "ERROR ~ fromIndex = -1"
Command used and terminal output
NXF_VER=23.04.1 /config/binaries/nextflow/23.04.1/nextflow run nf-core/nascent -profile singularity \
--input /scratch/teams/dawson_genomics/Projects/MYC/230427_PROseq/scripts/samplesheet.csv \
--outdir /scratch/teams/dawson_genomics/Projects/MYC/230427_PROseq/nf-core_nascent \
--genome GRCh38 \
--aligner bwamem2 \
--multiqc_title nf-core_nacent_multiqc \
--assay_type PROseq \
-resume
ERROR ~ fromIndex = -1
-- Check script '/home/agillespie/.nextflow/assets/nf-core/nascent/./workflows/nascent.nf' at line: 222 or see '.nextflow.log' file for more detailsRelevant files
System information
Nextflow version: 23.04.1
Hardware: HPC
Executor: slurm
Container: singularity
OS: CentOS 7 Linux
nf-core/nascent v2.1.1-g9ff33c7
samtools version: 1.17