When I used a UCSC gtf file and fasta file (genome.fa) to run tophat2, I was able to run it without any problems.
However, when I used a NONCODE mouse mm10 gtf file and NONCODE mouse fa file downloaded from http://www.noncode.org/download.php, I got “Error: Couldn't build bowtie index with err = 1” as follows:
[2016-06-30 00:49:29] Beginning TopHat run (v2.0.10) ----------------------------------------------- [2016-06-30 00:49:29] Checking for Bowtie Bowtie version: 188.8.131.52 [2016-06-30 00:49:29] Checking for Samtools Samtools version: 0.1.18.0 [2016-06-30 00:49:29] Checking for Bowtie index files (genome).. [2016-06-30 00:49:29] Checking for reference FASTA file [2016-06-30 00:49:29] Generating SAM header for Bowtie2Index/genome [2016-06-30 00:49:32] Reading known junctions from GTF file [2016-06-30 00:49:35] Preparing reads left reads: min. length=50, max. length=50, 29800718 kept reads (16597 discarded) [2016-06-30 00:54:48] Building transcriptome data files ./result/346_mm10/tmp/NONCODE2016_mouse_mm10_lncRNA [2016-06-30 00:54:51] Building Bowtie index from NONCODE2016_mouse_mm10_lncRNA.fa [FAILED] Error: Couldn't build bowtie index with err = 1
I renamed the NONCODE mouse fa file as genome.fa in the Bowtie2Index/ directory and kept the other 7 existing files (all have base name “genome”: genome.1.bt2, genome.3.bt2, genome.rev.1.bt2, genome.2.bt2, genome.4.bt2, genome.fa.fai, genome.rev.2.bt2) from the previous UCSC Bowtie2Index/ directory. I am wondering if this may cause any problems?
I also tried (in the Bowtie2Index/ directory):
bowtie-inspect -n genome
and got the following error message:
Could not locate a Bowtie index corresponding to basename "genome"
I also tried this command in the original UCSC Bowtie2Index/ directory but got the same above error message even though tophat2 runs fine with the UCSC data.
I would really appreciate any solution for this problem.
Thank you very much!