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(ERR): bowtie2-align exited with value 1

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
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updated by luzglongoria • luzglongoria • written by vahid.jj2005 • vahid.jj2005

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

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written by Ram Ram

TopHat is obsolete and the developers no longer recommend that anyone use it.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

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written by Brian Bushnell Brian Bushnell

Hi!

I'am very new in bioinformatic and I have a similar error but I'm using bowtie2. Here is my script:

 bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace/referencegenome/sturnus_relictumgenome.fasta -q -k 1 --al aligned_reads.fq -U /home/luz_garcia_longoria/workspace/*.fq > aligned_host_parasite.sam
Warning: Output file '/home/luz_garcia_longoria/workspace/s22_2.fq' was specified without -S.  This will not work in future Bowtie 2 versions.  Please use -S instead.
Extra parameter(s) specified: "/home/luz_garcia_longoria/workspace/s23_1.fq", "/home/luz_garcia_longoria/workspace/s23_2.fq", "/home/luz_garcia_longoria/workspace/s24_2.fq", "/home/luz_garcia_longoria/workspace/s25_1.fq", "/home/luz_garcia_longoria/workspace/s25_2.fq", "/home/luz_garcia_longoria/workspace/s31_1.fq", "/home/luz_garcia_longoria/workspace/s31_2.fq", "/home/luz_garcia_longoria/workspace/s32_1.fq", "/home/luz_garcia_longoria/workspace/s32_2.fq", "/home/luz_garcia_longoria/workspace/s33_1.fq", "/home/luz_garcia_longoria/workspace/s34_1.fq", "/home/luz_garcia_longoria/workspace/s34_2.fq", "/home/luz_garcia_longoria/workspace/s35_1.fq", "/home/luz_garcia_longoria/workspace/s35_2.fq"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /var/bin/bowtie2-2.3.1/bowtie2-align-s --wrapper basic-0 --threads 4 --local -x /home/luz_garcia_longoria/workspace/referencegenome/sturnus_relictumgenome.fasta -q -k 1 --passthrough -U /home/luz_garcia_longoria/workspace/s22_1.fq /home/luz_garcia_longoria/workspace/s22_2.fq /home/luz_garcia_longoria/workspace/s23_1.fq /home/luz_garcia_longoria/workspace/s23_2.fq /home/luz_garcia_longoria/workspace/s24_2.fq /home/luz_garcia_longoria/workspace/s25_1.fq /home/luz_garcia_longoria/workspace/s25_2.fq /home/luz_garcia_longoria/workspace/s31_1.fq /home/luz_garcia_longoria/workspace/s31_2.fq /home/luz_garcia_longoria/workspace/s32_1.fq /home/luz_garcia_longoria/workspace/s32_2.fq /home/luz_garcia_longoria/workspace/s33_1.fq /home/luz_garcia_longoria/workspace/s34_1.fq /home/luz_garcia_longoria/workspace/s34_2.fq /home/luz_garcia_longoria/workspace/s35_1.fq /home/luz_garcia_longoria/workspace/s35_2.fq 
(ERR): bowtie2-align exited with value 1

Please, I need some help!

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updated by GenoMax GenoMax • written by luzglongoria • luzglongoria

Please do not add an answer unless you're answering the top level question. Delete your post, then open a new question and mention that the top level post did not resolve your problem. Also, please use the formatting bar (especially the code option) to present your post better.
code_formatting

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written by Ram Ram

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

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written by amitunited0532 • amitunited0532

1 answer

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.

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written by Satyajeet Khare Satyajeet Khare

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

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written by vahid.jj2005 • vahid.jj2005

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