bowtie2: error reading ebwt[] array

[MatthewStoll]

Hi all,

I just downloaded bowtie2 into my cluster environment, along with the human genomic file. My command was: bowtie2 -f -x /scratch/user/mstoll/bowtie2/bowtie2-2.1.0/indexes/hg18 -U sample_data.fasta

The error message reads: Error reading _ebwt[] array: 129105920, 956874752
Error: Encountered internal Bowtie 2 exception (#1)

A similar problem was discussed on this forum about three years ago, and the suggestion was raised that the files could be corrupt. I re-ran the make_hg18.sh script, but that didn't solve the problem. Not sure how to tell if the file is corrupt.

[ctseto]

md5sum is one way to check the integrity of files.

Depending on the operating system, do md5sum

md5sum hg18.zip
b28f0d75c03356cd2328d8c47f6e06d4  hg18.zip

md5sum *hg18*
008ae77d5a382da10dd11f566b643e98  hg18.1.bt2
3e7f36b2918c7baed41e60e3f1d27ea5  hg18.2.bt2
428247833fa95a4b4245217b1e93d748  hg18.3.bt2
b5fc98dab658a66d93c3c4e8e09a4d8b  hg18.4.bt2
8967e67da16afdb93b2df34717b37e20  hg18.rev.1.bt2
b15cd42bcbbccdabff230a89e8744f82  hg18.rev.2.bt2
b28f0d75c03356cd2328d8c47f6e06d4  hg18.zip
98fa98b7a0f8ec91d3557f6c8ae5e24a  make_hg18.sh

Running the script should have worked, since it'll regenerate from ucsc hg18 files. It could point to an issue in bowtie2. Did the test datasets in bowtie2 work?

The bowtie2 directory has a subdirectory examples, broken up into reads, index and reference.

cd into index and run the following

../../bowtie2 -x lambda_virus -1 ../reads/reads_1.fq -2 ../reads/reads_2.fq -S /dev/null
10000 reads; of these:
  10000 (100.00%) were paired; of these:
    834 (8.34%) aligned concordantly 0 times
    9166 (91.66%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    834 pairs aligned concordantly 0 times; of these:
      42 (5.04%) aligned discordantly 1 time
    ----
    792 pairs aligned 0 times concordantly or discordantly; of these:
      1584 mates make up the pairs; of these:
        1005 (63.45%) aligned 0 times
        579 (36.55%) aligned exactly 1 time
        0 (0.00%) aligned >1 times
94.97% overall alignment rate

Likely the above will work if your copy of bowtie2 is fine.