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Question: Building Bowtie index, failed
1
gravatar for jingshuowang
3.9 years ago by
jingshuowang • 10
Germany
jingshuowang • 10 wrote:

I encountered a problem when trying to mapping RNA-seq reads to the genome.

Fatal error: Tool execution failed

[2015-01-02 07:08:06] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2015-01-02 07:08:06] Checking for Bowtie
    Bowtie version:  2.1.0.0
[2015-01-02 07:08:06] Checking for Samtools
  Samtools version:  0.1.18.0
[2015-01-02 07:08:06] Checking for Bowtie index files (genome)..
[2015-01-02 07:08:06] Checking for reference FASTA file
[2015-01-02 07:08:06] Generating SAM header for /galaxy/data/rheMac3/bowtie2_index/rheMac3

 format:   fastq
quality scale:  phred33 (default)
[2015-01-02 07:08:20] Reading known junctions from GTF file
[2015-01-02 07:08:29] Preparing reads
  left reads: min. length=101, max. length=101, 3322687 kept reads (9 discarded)
right reads: min. length=101, max. length=101, 3322669 kept reads (27 discarded)
[2015-01-02 07:10:46] Building transcriptome data files..
[2015-01-02 07:11:09] Building Bowtie index from dataset_10111788.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1

The gene annotation file (gff format, then converted to gtf) was downloaded from ENSEMBL.

Does anyone have some suggestions on this issue? Thanks a lot!
gff tophat alignment rna-seq • 4.2k views
ADD COMMENT • link •
modified 3.9 years ago by Bjoern Gruening ♦ 5.1k • written 3.9 years ago by jingshuowang • 10
1
gravatar for Bjoern Gruening
3.9 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

can you please check if your genome has the same labelling than your gtf file? If you genome is from UCSC and your annotation is from ENSEMBL this will not work.

Hope this helps,

Bjoern
ADD COMMENT • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k

Thank you Bjoern, this worked for me...

I made the error of trying to mix a UCSC index and an ENSEMBL GTF file.

The latest UCSC GTF file(s) can be gotten here: http://www.gencodegenes.org/releases/21.html

Once I downloaded the UCSC GTF file, TopHat appears to be working just fine.

Grateful;

DS

ADD REPLY • link written 3.9 years ago by Data Serf • 0

Nice! Can you please mark this answer as solved, this will help others to find help faster. Thanks.

ADD REPLY • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k
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