bowtie could not build the index

Question

[zizigolu]

Sorry guys,

I was building transcriptome index: I have yeast_SGD_anno.gtf and orf_coding.fasta as input which are in bowtie2 folder, then I typed:

[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat2 -G yeast_SGD_anno.gtf --transcriptome-index=transcriptome coding      

[2015-09-03 11:01:44] Building transcriptome files with TopHat v2.1.0
-----------------------------------------------
[2015-09-03 11:01:44] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-03 11:01:44] Checking for Bowtie index files (genome)..
[2015-09-03 11:01:44] Checking for reference FASTA file
    Warning: Could not find FASTA file coding.fa
[2015-09-03 11:01:44] Reconstituting reference FASTA file from Bowtie index
  Executing: ./bowtie2-inspect coding > ./tophat_out/tmp/coding.fa
[2015-09-03 11:01:45] Building transcriptome data files transcriptome/yeast_SGD_anno
[2015-09-03 11:01:45] Building Bowtie index from yeast_SGD_anno.fa
    [FAILED]
Error: Couldn't build bowtie index with err = 1
[izadi@lbox161 bowtie2-2.2.5]$

What happened please?

And when I changed the reference to Saccharomyces_cerevisiae.R64-1-1.pep.all.fa downloaded from http://www.ensembl.org/info/data/ftp/index.html, this is the result

[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat2 -G yeast_SGD_anno.gtf --transcriptome-index=transcriptome pep

[2015-09-03 11:35:33] Building transcriptome files with TopHat v2.1.0
-----------------------------------------------
[2015-09-03 11:35:33] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-03 11:35:33] Checking for Bowtie index files (genome)..
[2015-09-03 11:35:33] Checking for reference FASTA file
    Warning: Could not find FASTA file pep.fa
[2015-09-03 11:35:33] Reconstituting reference FASTA file from Bowtie index
  Executing: ./bowtie2-inspect pep > ./tophat_out/tmp/pep.fa
    [FAILED]
Error: bowtie-inspect returned an error
bowtie-inspect: bt2_inspect.cpp:234: void print_ref_sequences(std::ostream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const TIndexOffU*, const std::string&): Assertion `0' failed.

[izadi@lbox161 bowtie2-2.2.5]$

Help me please

Thank you

[5heikki]

orf_coding.fasta as input

Warning: Could not find FASTA file coding.fa

Saccharomyces_cerevisiae.R64-1-1.pep.all.fa

Warning: Could not find FASTA file pep.fa

The error messages seem rather self-explanatory to me..

[zizigolu]

sorry but there is the fasta file there...please tell me more

if it is because of not matching in gtf and genome reference??? if so how i can find these matched files?

[5heikki]

You wrote that you used orf_coding.fasta as input file but the program is saying that it was called with coding.fa as input file. Same with the other example. The names don't match.