#265 bowtie2-build failed

v0.9.0
closed
Val
5
2014-07-23
2013-01-09
No

boetie3-build failed, and there's a core dump. Here's the output:

chr[$]: 2934502525
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 982388725 bytes to primary EBWT file: hs_bowtie2.1.bt2
Wrote 733625636 bytes to secondary EBWT file: hs_bowtie2.2.bt2
*** glibc detected *** bowtie2-build: free(): invalid next size (normal): 0x000$
======= Backtrace: =========
/lib64/libc.so.6[0x370a87245f]
/lib64/libc.so.6(cfree+0x4b)[0x370a8728bb]
/usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE26_M_destroy$
/usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE5closeEv+0x6$
bowtie2-build[0x430114]
bowtie2-build[0x40b6b9]
bowtie2-build[0x40ea34]
bowtie2-build[0x458bce]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x370a81d994]
bowtie2-build(__gxx_personality_v0+0x109)[0x4034f9]

Running `uname -a` gives

Linux n002.local 2.6.18-274.el5 #1 SMP Fri Jul 8 17:36:59 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux

I can upload the core dump if you need it.

Thanks!

Discussion

  • Ben Langmead
    Ben Langmead
    2013-01-27

    Dear Tianyang,

    Thank you for the report. Yes, a core dump would be helpful. Also, if would be helpful if you could share (or tell us where to get) the reference file(s) you're indexing.

    Best,
    Ben

     
  • Ben Langmead
    Ben Langmead
    2013-01-27

    • status: open --> pending
     
  • I was indexing hg19.

     
    • status: pending --> open
     
  • I'll try to upload the core dump to another place, uploading it to SF has failed several times.

     
  • Here's the [core dump](http://tianyang-files.googlecode.com/files/core.3474).

     
  • Val
    Val
    2014-07-23

    • status: open --> closed
    • assigned_to: Val
    • Group: --> v0.9.0
     
  • Val
    Val
    2014-07-23

    Large index support might solve this issue now.