Please tell me what's wrong with my tophat script?

Question

[abdul.suboor123]

I am trying to find the unmapped reads by fusion-search in tophat, but When submit the command it shows some sort of warning, code is given below.

[skabdul@node102 Mo17]$ sh tophat.sh

[2018-11-06 20:00:15] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-11-06 20:00:15] Checking for Bowtie
          Bowtie version:    1.1.2.0
[2018-11-06 20:00:16] Checking for Bowtie index files (genome)..
[2018-11-06 20:00:16] Checking for reference FASTA file
    Warning: Could not find FASTA file ../Mo17/Ref-index.fa
[2018-11-06 20:00:16] Reconstituting reference FASTA file from Bowtie index
  Executing: /public/home/software/opt/bio/software/Bowtie/1.1.2-foss-2016b/bin/bowtie-inspect ../Mo17/Ref-index > M1_tophat_fusion/tmp/Ref-index.fa

Also check the command if there is something wrong in it or not?

/tophat-2.1.1.Linux_x86_64/tophat -o M1_tophat_fusion -p 12 --fusion-search --bowtie1 --keep-fasta-order --no-coverage-search ../Mo17/Ref-index M1_PE400_R1.fq M1_PE400_R2.fq

[ATpoint]

I just drop this post from the senior developer here, so you may consider to change to a more recent tool like STAR or HISAT2.

[cpad0112]

I think op is looking for fusion transcripts, which hisat lacks as of now. May be that user can use star fusion

[abdul.suboor123]

I think there is no star-fusion , I am using tophat for circexplorer2 software, I search that websiter, the pipeline has not star-fusion.

[cpad0112]

https://github.com/STAR-Fusion/STAR-Fusion/wiki

[abdul.suboor123]

I am looking for fusion search to collect the unmapped reads. Its very slow I dont know whats the problem.

[cpad0112]

are these solid reads? If not, let tophat use bowtie 2 instead of bowtie 1.

Answer 1

[WouterDeCoster]

The warning message is really clear:

Tophat expects to find ../Mo17/Ref-index.fa, but the fasta file is not there. Therefore it recreates the fasta file based on the Bowtie index. Everything runs normally.

[abdul.suboor123]

Thanks, but i have reference in fasta format. Then why it shows this warning? and tell me please it will create any problem? because even it shows warning but the program i running normally.

[WouterDeCoster]

So you mean that ../Mo17/Ref-index.fa does exist? But no, this warning causes no problem. It just will run a bit slower because the fasta file has to be recreated from the indices.

For the record, I don't consider myself a "bro", but if that's how you want to address people online then go ahead.

[abdul.suboor123]

Sorry for saying bro, It runs very slower, I have start running this job almost 12 hours ago, but till now it is running , I added -p 12 but with 12 cpu it is still very slow. Can you please mention how much time it takes normally?