Problem with mirdeep2: The mapped reference id from refdb.arf is not an id of the genome fasta file

Question

[otieno43]

Hi everyone, I'm trying to run mirdeep2 pipeline and I'm having a problem. I have initially ran it successfully a couple of times but now I get some issues.

Command:

/home/ea432/.conda/envs/umi_mir/bin/miRDeep2.pl \
  /gpfs/gibbs/project/ea432/Gff_midgut/MiRNA/Results/Mapper_results/GmMG_cat-reads_collapsed.fa \
  /gpfs/gibbs/project/ea432/Genomes/VectorBase-65_GmorsitansYale_Genome1.fasta \
  /gpfs/gibbs/project/ea432/Gff_midgut/MiRNA/Results/Mapper_results/GmMG_cat-reads_vs_refdb.arf \
  /gpfs/gibbs/project/ea432/Genomes/Gmm_miRNA.fasta \
  /gpfs/gibbs/project/ea432/Genomes/erick_MirBase_sorted.fa \
  /gpfs/gibbs/project/ea432/Genomes/erick_hairpin_sorted.fa

The error I get is this:

The mapped reference id GmorY1_scf7180000638812 from file /gpfs/gibbs/project/ea432/Gff_midgut/MiRNA/Results/Mapper_results/GmMG_cat-reads_vs_refdb.arf is not an id of the genome file /gpfs/gibbs/project/ea432/Genomes/VectorBase-65_GmorsitansYale_Genome1.fasta

I have tried to look at solution online in this forum and others and it seems I do not get to solve this. Any help please.

Thank you