Question: (ERR): bowtie2-align exited with value 1
0
gravatar for vahid.jj2005
2.4 years ago by
vahid.jj20050 wrote:

Hi I have a problem when run tophat. I have recieved this massage:

Error running bowtie: 
Warning: output file '-' was specified without -s. This will not work in future Bowtie 2 versions. Please us -s instead. 
Warning: could not open read file "/1AM21/tophat1/tmp/index" for reading; skipping... 
Error: no input read files were valid.
(ERR): bowtie2-align exited with value 1

Please help me!!!

rna-seq software error • 2.4k views
ADD COMMENTlink modified 16 months ago by luzglongoria40 • written 2.4 years ago by vahid.jj20050
1

TopHat is obsolete and the developers no longer recommend that anyone use it. I suggest you use a different aligner such as Star or BBMap.

ADD REPLYlink written 2.4 years ago by Brian Bushnell17k

What is the exact command you ran? Before you paste that here, ensure you run it again and get the exact same error message.

ADD REPLYlink written 2.4 years ago by RamRS25k

![please see this picture] https://ibb.co/msadyk

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by vahid.jj20050

Use Hisat2, it is better and fast. or If you have better computational facility, go for STAR aligner. (Required at least 32GB RAM)

I don't recommend Bowtie2 or tophat for your work. All the best

ADD REPLYlink written 16 months ago by amitunited053210
1
gravatar for Satyajeet Khare
2.4 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:

Vahid, few things.

  1. Avoid space in your directory. That is change /medicago / to /medicago/
  2. You are running Tophat2 so your output directory needs to be /tophat2/
  3. Try without GTF file and default settings first (without --read edit options).

Lets see if that produces an error.

ADD COMMENTlink written 2.4 years ago by Satyajeet Khare1.5k

Thank Satyajeet. Your advice were correct. Best Regards, Vahid

ADD REPLYlink written 2.4 years ago by vahid.jj20050
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