Error: Encountered internal Bowtie 2 exception (#1)- Error reading _ebwt[] array: no more data

[jefferyUstc]

Hi Bowtie2 team, i built a large bowtie2 index for mapping reads.

total 133435644
-rw-rw----+ 1 jeff nobody 43675027048 Sep 15 00:56 ref_index.1.bt2l
-rw-rw----+ 1 jeff nobody 23019217540 Sep 15 00:55 ref_index.2.bt2l
-rw-rw----+ 1 jeff nobody 20060349498 Sep 14 16:05 ref_index.3.bt2l
-rw-rw----+ 1 jeff nobody 11509608764 Sep 14 16:05 ref_index.4.bt2l
-rw-rw----+ 1 jeff nobody 15354534352 Sep 15 09:29 ref_index.rev.1.bt2l
-rw-rw----+ 1 jeff nobody 23019217540 Sep 15 09:29 ref_index.rev.2.bt2l

## Log info for build the index (just show last lines of log)
Returning block of 461271466 for bucket 113
  bucket 119: 70%
  Sorting block time: 00:01:43
Returning block of 274052016 for bucket 116
  Sorting block time: 00:03:12
Returning block of 486340735 for bucket 110
  bucket 120: 100%
  Sorting block of length 181450669 for bucket 120
  (Using difference cover)
  bucket 118: 90%
  bucket 119: 80%
  bucket 118: 100%
  Sorting block of length 355040350 for bucket 118
  (Using difference cover)
  Sorting block time: 00:02:38
Returning block of 419608539 for bucket 117
  bucket 119: 90%
  Sorting block time: 00:01:05
Returning block of 181450670 for bucket 120
  bucket 119: 100%
  Sorting block of length 375196572 for bucket 119
  (Using difference cover)
  Sorting block time: 00:03:21
Returning block of 531786056 for bucket 115
  Sorting block time: 00:02:11
Returning block of 355040351 for bucket 118
  Sorting block time: 00:02:17
Returning block of 375196573 for bucket 119
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 11304538870
fchr[G]: 20200379535
fchr[T]: 35518546876
fchr[$]: 46038435056
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 125484427260 bytes to primary EBWT file: Results/origin/bowtie2_index/ref_index.rev.1.bt2l.tmp
Wrote 23019217540 bytes to secondary EBWT file: Results/origin/bowtie2_index/ref_index.rev.2.bt2l.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 46038435056
    bwtLen: 46038435057
    sz: 11509608764
    bwtSz: 11509608765
    lineRate: 7
    offRate: 4
    offMask: 0xfffffffffffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 160
    ftabLen: 1048577
    ftabSz: 8388616
    offsLen: 2877402192
    offsSz: 23019217536
    lineSz: 128
    sideSz: 128
    sideBwtSz: 96
    sideBwtLen: 384
    numSides: 119891758
    numLines: 119891758
    ebwtTotLen: 15346145024
    ebwtTotSz: 15346145024
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 03:02:05

It looks everything fine for the index. However, when I try to map the reads with the index. It raised an problem:

Error reading _ebwt[] array: no more data
Error: Encountered internal Bowtie 2 exception (#1)
Command: /path/to/bowtie2-2.5.3-linux-x86_64/bowtie2-align-l --wrapper basic-0 -p 2 -x Results/ligation/bowtie2_index/ref_index -f -S Results/barcodeFasta/test.sam --sensitive Results/barcodeFasta/test.fasta
(ERR): bowtie2-align exited with value 1

Do you have some insights or suggestions for me? Thank you.

[ch4rr0]

Hello,

There must have been some sort of I/O issue while reading the BWT. Does this happen consistently? Are you reading the data off of a local filesystem?