TopHat Error: Couldn't build bowtie index with err = -11

Question

[Sun Jiji]

When I was running tophat, I met this problem:

Error: Couldn't build bowtie index with err = -11

It seemed that it was because of the differences between the annotation and index.

But I tried different annotation files, all return the same error -11

Here are annotation and index I tried

1. illumina iGenomes, UCSC hg38

2. illumina iGenomes, NCBI GRCh38

3. illumina iGenomes, Ensembl GRCh37

4. Gencode Release 28 (GRCh38.p12) (annotation) and bowtie pre-built index NCBI GRCh38

Here is the call

root@DESKTOP-2SILU7S:/mnt/c/ubuntu# tophat --bowtie1 -p 8 -o ./tophat_out_Control_1 -G ./bowtie_indexes/GRCh38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes.gencode/genes.gtf ./bowtie_indexes/GRCh38/Sequence/BowtieIndex/genome ./Control_1_1_filtered.fastq

Here is the error

[2018-08-16 14:41:23] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-08-16 14:41:23] Checking for Bowtie
                  Bowtie version:        1.2.2.0
[2018-08-16 14:41:23] Checking for Bowtie index files (genome)..
[2018-08-16 14:41:23] Checking for reference FASTA file
[2018-08-16 14:41:23] Generating SAM header for ./bowtie_indexes/GRCh38/Sequence/BowtieIndex/genome
[2018-08-16 14:41:40] Reading known junctions from GTF file
[2018-08-16 14:42:09] Preparing reads
         left reads: min. length=18, max. length=101, 56278536 kept reads (13726 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
[2018-08-16 15:01:09] Building transcriptome data files ./tophat_out_Control_1/tmp/genes
[2018-08-16 15:02:25] Building Bowtie index from genes.fa
        [FAILED]
Error: Couldn't build bowtie index with err = -11

[h.mon]

TopHat has been retired, see note at TopHat site:

Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.

Or this tweet from one of the original TopHat authors:

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[Sun Jiji]

I use tophat2 and bowtie2, and use the illumina NCBI GRCh38 index, it really works.Thank you.