Forgotten command line argument leads to an error message from miRDeep2.pl

[annefleurbrand]

Hello,

I installed miRdeep2 as per the instructions on this platform and the mapper.pl and quantifier.pl functions work perfectly. However, when running mirdeep.pl, my MiRBase input files do not seem to be recognised and I get the following error:

Error: no file containing miRNAs precursors of investigating species specified

Either specify a valid fasta file or say none

The first three arguments to miRDeep2.pl must be files while arguments 4-6 can be files or must be designated as 'none'. Examples:

miRDeep2.pl reads.fa genome.fa reads_vs_genome.arf mautre_ref_miRNAs.fa mature_other_miRNAs.fa hairpin_ref_miRNAs

or

miRDeep2.pl reads.fa genome.fa reads_vs_genome.arf none none none

Please check if the supplied files exist and the command call to miRDeep2.pl is correct

My code:

/home2/fleur/mirdeep2/bin/miRDeep2.pl /home2/fleur/Mapping/BIRDS_pool_processed.fa \
/home2/fleur/Genomes/new_Chicken.fa /home2/fleur/Genomes/BIRDS_pool_mapped_Chicken.arf \
/home2/fleur/MiRBase/gga_matureMiRNA.fa /home2/fleur/MiRBase/gga_hairpinMiRNA.fa -t gga -z .initialPred  \
> miRdeep2.log 2> miRdeep2.err &

It does run when I remove the miRBase .fa files or when I replace them with none.

I tried the code with -P and without -P and different approaches for miRBase data preprocessing:

extract_miRNAs.pl /home2/fleur/MiRBase/mature.fa apl,cli,gga,tgu > mature_birds.fa
extract_miRNAs.pl /home2/fleur/MiRBase/hairpin.fa apl,cli,gga,tgu > hairpin_birds.fa

Download mirBase mature and precursor sequences

wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz
wget ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz

Remove white space

zcat hairpin.fa.gz | cut -f1 -d" ">/home2/fleur/MiRBase//hairpin_noSpace.fa
zcat mature.fa.gz | cut -f1 -d" " >/home2/fleur/MiRBase//mature_noSpace.fa

Remove non-canonical nucleotides and convert to SL

fastaparse.pl /home2/fleur/MiRBase//hairpin_noSpace.fa -b | fasta_formatter -w 0  >hairpin_cleaned.fa
fastaparse.pl /home2/fleur/MiRBase//mature_noSpace.fa -b | fasta_formatter -w 0 >mature_cleaned.fa

Select chicken miRNAs ..

grep -A1 "gga" mature_cleaned.fa  | grep -v -- "^--$" >gga_matureMiRNA.fa
grep -A1 "gga" hairpin_cleaned.fa | grep -v -- "^--$" >gga_hairpinMiRNA.fa

I'm sorry if I'm overlooking something very basic... Thank you in advance for any help you can provide!

[annefleurbrand]

Apologies, I just worked it out... The files are recognised when I insert "none" between/after the input files.

/home2/fleur/mirdeep2/bin/miRDeep2.pl /home2/fleur/Mapping/BIRDS_pool_processed.fa /home2/fleur/Genomes/new_Chicken.fa \
/home2/fleur/Genomes/BIRDS_pool_mapped_Chicken.arf /home2/fleur/MiRBase/gga_matureMiRNA.fa none /home2/fleur/MiRBase/hairpin_birds.fa -t gga -z .initialPred

[Drmirdeep]

Great. Now it would be kind if you let other people know what the exact issue was and what you did to solve it.