Checking Aligner-bowtie1index parameter ... error!

[flyman0302]

[Wed Nov 29 11:06:10 2017] Starting a miARma analysis for miRNA [Wed Nov 29 11:06:10 2017] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction. [Wed Nov 29 11:06:10 2017] Checking Aligner-bowtie1index parameter ... error! ERROR Please check that the parameter bowtie1index inside section [Aligner] is correct.

[Eduardo Andres Leon]

Did you save index files for your genome in the folder indicated in the bowtie1index parameter ?

[Gabe]

I'm receiving the same error and I've been chasing my tail for two days trying to resolve it. I have the index files saved in the folder indicated in the bowtie1index parameter and I've verified that permissions are correct for accessing that folder location.

[Eduardo Andres Leon]

Remember than you have to specify the folder and the base name of the index. If you take look to the webpage (http://miarmaseq.idoproteins.com/usage):

[Aligner]
; Aligner to use with miRNA (Bowtie1, Bowtie2, BWA or miRDeep)
aligner=Bowtie1
bowtie1index=/Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19

You will see /Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19. So in the /Genomes/Indexes/bowtie1/human/ you must have the following files:

bw1_homo_sapiens19.1.ebwt
bw1_homo_sapiens19.2.ebwt
bw1_homo_sapiens19.3.ebwt
bw1_homo_sapiens19.4.ebwt
bw1_homo_sapiens19.rev.1.ebwt
bw1_homo_sapiens19.rev.2.ebwt

[Gabe]

Thank you so much Eduardo. That was my issue. I had the files you specified within a directory named bw1_homo_sapiens19, not within the human directory. Much appreciated!