I am working with pepper genome Capsicum annuum zunla variety (http://peppersequence.genomics.cn/page/species/download.jsp). I was aligning the RNA-seq reads to this genome with the following command,
tophat2 -p 6 --min-intron-length 40 --bowtie-n --no-novel-juncs --b2-very-sensitive -G /Volumes/Pepper_Tosh/TOPHAT/CaZL1.gff BOWTIE2_INDEXES/capsicumgenome2 PT_8h_5_S30_combined_R1_001_trimmed.fastq
But, somehow I am getting the following error, [2017-08-03 15:37:14] Beginning TopHat run (v2.0.14)
[2017-08-03 15:37:14] Checking for Bowtie
Bowtie version: 22.214.171.124
[2017-08-03 15:37:14] Checking for Bowtie index files (genome)..
[2017-08-03 15:37:14] Checking for reference FASTA file
[2017-08-03 15:37:14] Generating SAM header for BOWTIE2_INDEXES/capsicumgenome2
[2017-08-03 15:37:19] Reading known junctions from GTF file
[2017-08-03 15:37:20] Preparing reads
left reads: min. length=12, max. length=111, 19832519 kept reads (5687 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2017-08-03 15:45:29] Building transcriptome data files ./tophat_out/tmp/CaZL1
[2017-08-03 15:46:02] Building Bowtie index from CaZL1.fa
Error: Couldn't build bowtie index with err = 1
I think the gff file of my genome is not optimum here to run. The gff file I used is downloaded from the below link,
http://peppersequence.genomics.cn/page/species/download.jsp and the name of file is - Capsicum.annuum.L_Zunla-1_v2.0_genes.gff.gz
Can please someone help me to figure out what is exactly going wrong??
Thank you very much in advance.