(ERR): bowtie2-align exited with value 1

Question

[vahid.jj2005]

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!!!

[Brian Bushnell]

TopHat is obsolete and the developers no longer recommend that anyone use it.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.

[Ram]

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

[vahid.jj2005]

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

[amitunited0532]

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

Answer 1

[Satyajeet Khare]

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.

[vahid.jj2005]

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