tophat2 bowtie2index error

Question

[dimitrischat]

hi all, trying to run tophat2 , with -G xx.gtf and bowtie2index. the command is :

tophat2 --library-type fr-unstranded -g 1 -G /home/..../**Homo_sapiens.GRCh38.90.gtf** /home/..../Homo_sapiens/UCSC/hg38/Sequence/**Bowtie2Index/genome** /home/.../xx.fastq

The error :

Building Bowtie index from Homo_sapiens.GRCh38.90.fa
    [FAILED]
Error: Couldn't build bowtie index with err = 1

Same command was used for mouse and it worked. Also changed the gtf file and placed it into the same folder as the bowtie2index and it didnt work ( as i read a suggestion here )

edit: why is it trying to create Bowtie2index from the gtf file while i specified the index file!!

[GenoMax]

Because you specificed the -G option.

-G/--GTF <gtf gff3="" file="">

Supply TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output.

Check the --transcriptome-index option below the one for -G in tophat manual here.