Hi, the following bug was discussed on the Slack #rnaseq channel (4th March) and a workaround was identified.
When trying to use salmon pseudo-mapping quantification, an error asking to add "--bam_csi_index" because of long chromosomes will show up, despite the parameter being already mentionned.
This issue does not appear on v3.5.
Command used and terminal output
nextflow run nf-core/rnaseq -profile docker --input samplesheet.csv --fasta psat_genome.fa --gtf psat_annotation.gtf --pseudo_aligner salmon --skip_alignment --bam_csi_index --outdir results_rnaseq/henriet2019_sample
Contig longer than 512000000bp found in reference genome!
chr5LG3: 579269071
Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.
Please see:
https://github.com/nf-core/rnaseq/issues/744
drpatelh
commented
2 years ago
Description of the bug
Hi, the following bug was discussed on the Slack #rnaseq channel (4th March) and a workaround was identified. When trying to use salmon pseudo-mapping quantification, an error asking to add "--bam_csi_index" because of long chromosomes will show up, despite the parameter being already mentionned. This issue does not appear on v3.5.
Command used and terminal output
Relevant files
No response
System information
Nextflow version 21.10.6 nf-core/rnaseq 3.6