Tophat: bowtie indexing error

Question

[ChillarAnand]

Error Message

Couldn't build bowtie index with err = 1

Previous discussions suggests these

• use both reference genome and gtf from the same source
• issue can be with terminology "chr#1" in fasta and "1" in gtf

We have tried previously suggested options, but none seems to be useful in the context.

P.S: We are analysing Anophele stephensi (not so general species of anopheles) and vectorbase being the source.

Thank you for all suggestions and comments !!

Update:

Version: bowtie==2..2.6

Command: tophat2 -p 7 -T -G ../../anapholes_stephensi/reference/stephnsi.gtf -o tophat_gtf_out/ ../../anapholes_stephensi/reference/stephensi 1_cutadapt.fastq 2_cutadapt.fastq

Fasta file: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000300775.2_ASM30077v2/GCA_000300775.2_ASM30077v2_genomic.fna.gz

[Devon Ryan]

Can you post the following?

1. The version of bowtie (or bowtie2)
2. The exact command you're using
3. The URL to the fasta file(s)

bowtie/bowtie2 don't use GTF files and also aren't the best choice for RNAseq since they can't handle splicing. Are you instead using tophat2 (yes, this uses bowtie internally)? If so, which version?

[ChillarAnand]

Added details in question. Thanks.

[GenoMax]

Can you post the full log output?

e.g. like here