Getting: Error reading _plen[] array: 1776466139, 4294967292 with TopHat2/bowtie2

Question

[rubic]

Hi,

I think seem to be doing something very basically wrong in running TopHat2 so it's probably an easy answer.

Here's my command:

tophat \
  --read-mismatches 1 \
  --output-dir /n/user/rubi/data/tophat.alns/s1/s1 \
  --num-threads 8 \
  --transcriptome-index /n/user/rubi/refdata/tophat.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 \
  /n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 \
  /n/user/rubi/data/fq/s1.fq

Here's the log file:

[2015-03-20 00:07:34] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2015-03-20 00:07:34] Checking for Bowtie
Bowtie version:  2.0.0.6
[2015-03-20 00:07:34] Checking for Samtools
Samtools version:  0.1.12.a
[2015-03-20 00:07:34] Checking for Bowtie index files
[2015-03-20 00:07:34] Checking for Bowtie index files
[2015-03-20 00:07:34] Checking for reference FASTA file
[2015-03-20 00:07:34] Generating SAM header for /n/user/rubi/refdata/tophat.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10
format:  fastq
quality scale:  phred33 (default)
[2015-03-20 00:07:35] Reading known junctions from GTF file
[2015-03-20 00:08:03] Preparing reads
 left reads: min. length=20, max. length=59, 128844351 kept reads (192369 discarded)
[2015-03-20 00:49:52] Using pre-built transcriptome index..
[2015-03-20 00:50:20] Mapping left_kept_reads to transcriptome mm10 with Bowtie2 
[2015-03-20 03:33:13] Resuming TopHat pipeline with unmapped reads
[2015-03-20 03:33:15] Mapping left_kept_reads.m2g_um to genome mm10 with Bowtie2 
[FAILED]
Error running bowtie:
Error reading _plen[] array: 1776466139, 4294967292
Error: Encountered internal Bowtie 2 exception (#1)
Command: /n/sw/bowtie2-2.0.0-beta6/bowtie2-align -q -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min L,-0.6,-0.6 -p 8 --sam-no-hd -x /n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 -

As far as I can tell BOWTIE_INDEXES is defined as an environment variable:

rubi@rclogin09 10:25 ~ >echo $BOWTIE_INDEXES
/n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10

And the transcriptome and genome index folders seem to be found - according to the log. So what's wrong?

[Devon Ryan]

This error has something to do with reading the index into memory. My guess would be that either you're running out of memory or that there's something wrong with one of the indices. In either case, try to delete and remake then genome index. BTW, you should really upgrade your versions of tophat2 and bowtie2.