Question: bowtie could not build the index
0
gravatar for F
2.8 years ago by
F3.0k
Iran
F3.0k wrote:

sorry guys,

i was building transcriptom 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

 

rna-seq tophat2 bowtie2 • 2.2k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by F3.0k
2

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..

 

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by 5heikki7.3k

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?

ADD REPLYlink written 2.8 years ago by F3.0k
1

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.

ADD REPLYlink written 2.8 years ago by 5heikki7.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 848 users visited in the last hour