Error bowtie1index and bowtie2index

[Former user]

I can't work out why I see this error. I also see it with example ini files so I think I'm doing something fundamentally wrong.

perl ./miARma config/config_v0.2.ini -check

gives:

ERROR Please check that the parameter fasta inside section [Aligner] is correct.

[Aligner]
; Aligner (Bowtie1, Bowtie2, BWA, miRDeep or Bowtie1-Bowtie2)
aligner=Bowtie2
; Path of the genomic fasta sequence to build the index
fasta=genomes/human/Bowtie2/genome.fa
;Name to write in the index files
indexname=genome
; #Max # mismatches in seed alignment in bowtie analysis (0-1)
bowtiemiss=0
; #Length of seed substrings in bowtie analysis (>5, <32)
bowtieleng=19

I also tried Bowtie 1:

[Aligner]
; Aligner (Bowtie1, Bowtie2, BWA or miRDeep)
aligner=Bowtie1
; Bowtie 2 index
bowtie1index=/home/miARma/miARma/genomes/human/BowtieIndex

And two:

[Aligner]
; Aligner (Bowtie1, Bowtie2, BWA or miRDeep)
aligner=Bowtie2
; Bowtie 2 index
bowtie2index=/home/miARma/miARma/genomes/human/Bowtie2Index

with ERROR Please check that the parameter bowtie1index inside section [Aligner] is correct. and ERROR Please check that the parameter bowtie2index inside section [Aligner] is correct. relatively

[Eduardo Andres Leon]

For indexes you have to write the name of the prefix name. That is the filename of the indexes without the extensions (bw2, eb …)