miRDeep2: Mapped reference id is not an id of the genome file genome_nowhitespace.fa

Question

[gkae]

Hi everyone, I'm trying to run nf-co.re/smrnaseq pipeline and I'm having a problem with mirdeep2.

Command:

nextflow run nf-core/smrnaseq -profile ijcluster --input /home/794_both.fastq.gz --outdir /home/results --genome GRCh38 --protocol qiaseq --mature https://mirbase.org/ftp/CURRENT/mature.fa.gz --hairpin https://mirbase.org/ftp/CURRENT/hairpin.fa.gz

Error message:

Command error:

#Starting miRDeep2
/opt/conda/envs/nf-core-smrnaseq-1.1.0/bin/miRDeep2.pl `794_both_trimmed_collapsed.fa genome_nowhitespace.fa 794_both_trimmed_reads_vs_refdb.arf mature.fa none hairpin_ok.fa -d -z _794_both_trimmed_collapsed

mkdir mirdeep_runs/run_01_04_2022_t_13_00_05_794_both_trimmed_collapsed

The mapped reference id chr1 from file 794_both_trimmed_reads_vs_refdb.arf is not an id of the genome file genome_nowhitespace.fa`

Does anyone have any idea what I can do to solve it? Any help / suggestions would be very appreciated! Thanks!

[Pierre Lindenbaum]

check you're using the right reference an look at the naming of the chromosomes ("chr1" vs "1") in the arf and the fasta

Answer 1

[apeltzer]

Please also take a look at the dev branch of the pipeline that contains a lot of improvements and bugfixes. You can also reach out on Slack https://nf-co.re/join (and then ask in the #smrnseq channel) or open a Github issue there to get some help https://github.com/nf-core/smrnaseq/issues/new

First try would be using the -r dev branch however - have a look at the docs on how to run it then https://nf-co.re/smrnaseq/dev