Mapping left_kept_reads.m2g_um to genome FAILED running Tophat2/Bowtie2

Question

[oestevez89]

Hi,

I am using Tophat (v2.0.14) to align my RNAseq reads to a reference genome (Human genome Hg38.82).

I have made the genome index using Bowtie (v2.2.5.0).

When I run tophat I get the following:

[2015-10-06 18:06:20] Beginning TopHat run (v2.0.14)
-----------------------------------------------
[2015-10-06 18:06:20] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-10-06 18:06:20] Checking for Bowtie index files (genome)..
[2015-10-06 18:06:20] Checking for reference FASTA file
[2015-10-06 18:06:20] Generating SAM header for /usr/local/cellar/bowtie2/2.2.5/bin/Indexes/Hg38.82
[2015-10-06 18:06:23] Reading known junctions from GTF file
[2015-10-06 18:07:43] Preparing reads
     left reads: min. length=20, max. length=360, 18238820 kept reads (111 discarded)
[2015-10-06 18:12:46] Building transcriptome data files /Users/emitb643558/desktop/RNAseq/tophat/tmp/Homo_sapiens.GRCh38.82.chr_patch_hapl_scaff
[2015-10-06 18:20:34] Building Bowtie index from Homo_sapiens.GRCh38.82.chr_patch_hapl_scaff.fa
[2015-10-06 18:44:16] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh38.82.chr_patch_hapl_scaff with Bowtie2 
[2015-10-06 19:03:07] Resuming TopHat pipeline with unmapped reads
[2015-10-06 19:03:08] Mapping left_kept_reads.m2g_um to genome Hg38.82 with Bowtie2 
    [FAILED]
Error running bowtie:
Error reading _plen[] array: 1027440330, 4294967292
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bin/../Cellar/bowtie2/2.2.5/bin/bowtie2-align-s --wrapper basic-0 -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 C,-14,0 -p 6 --sam-no-hd -x /usr/local/cellar/bowtie2/2.2.5/bin/Indexes/Hg38.82 - 
(ERR): bowtie2-align exited with value 1

Do anyone know why I am getting this error? Is the version of Tophat that I am using compatible with that of Bowtie? Could it be a problem with the indexed genome?

Thanks for your help.

Answer 1

[Pei]

Hi:

I have the similar error:

[2016-01-21 15:12:29] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2016-01-21 15:12:29] Checking for Bowtie
          Bowtie version:     2.2.1.0
[2016-01-21 15:12:30] Checking for Samtools
        Samtools version:     0.1.18.0
[2016-01-21 15:12:30] Checking for Bowtie index files (transcriptome)..
[2016-01-21 15:12:30] Checking for Bowtie index files (genome)..
[2016-01-21 15:12:30] Checking for reference FASTA file
[2016-01-21 15:12:30] Generating SAM header for hugenome
[2016-01-21 15:12:32] Reading known junctions from GTF file
[2016-01-21 15:13:00] Preparing reads
     left reads: min. length=76, max. length=76, 7805492 kept reads (107689 discarded)
[2016-01-21 15:14:24] Using pre-built transcriptome data..
[2016-01-21 15:14:28] Mapping left_kept_reads to transcriptome known with Bowtie2
[2016-01-21 15:16:45] Resuming TopHat pipeline with unmapped reads
[2016-01-21 15:16:46] Mapping left_kept_reads.m2g_um to genome hugenome with Bowtie2
    [FAILED]
Error running bowtie:
Error reading _plen[] array: 599200902, 4294967292
Error: Encountered internal Bowtie 2 exception (#1)
Command: /public1/users/linpei/software/bowtie2-2.2.1/bowtie2-align-s --wrapper basic-0 -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 C,-14,0 -p 16 --sam-no-hd -x hugenome -
(ERR): bowtie2-align exited with value 1

Did you, or anyone else, solve this problem ?

it seemed that changing to hg19 genome works fine.

Thanks,

Best