[wgs-assembler-users] Assertion failed in markRepeatUnique.C

[Ryo K. <koy...@oi...>]

Dear all.

I have been running CA 8.3 with a hybrid dataset, error-corrected PacBio
and 300bp paired illumina and got an assertion failed error from
markRepeatUnique.C as follows:

Command Line options:
  singleReadMaxCoverage    1.000000
  lowCoverage              2 coverage 1.000000 fraction
  minReads                 2
  tooLong                  4294967295
  tooShort                 1000
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Generating statistics.
markRepeatUnique: markRepeatUnique.C:352: int main(int, char**): Assertion
`ma->data.num_frags == GetNumIntMultiPoss(ma->f_list)' failed.

Failed with 'Aborted'

Backtrace (mangled):

/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique(_Z17AS_UTL_catchCrashiP7siginfoPv+0x2a)[0x40a49a]
/lib64/libpthread.so.0[0x37dae0f710]
/lib64/libc.so.6(gsignal+0x35)[0x37da632925]
/lib64/libc.so.6(abort+0x175)[0x37da634105]
/lib64/libc.so.6[0x37da62ba4e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x37da62bb10]
/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique(main+0x24cc)[0x40818c]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x37da61ed1d]
/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique[0x4083b9]

Backtrace (demangled):

[0]
/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique::AS_UTL_catchCrash(int,
siginfo*, void*) + 0x2a  [0x40a49a]
[1] /lib64/libpthread.so.0() [0x37dae0f710]
[2] /lib64/libc.so.6::(null) + 0x35  [0x37da632925]
[3] /lib64/libc.so.6::(null) + 0x175  [0x37da634105]
[4] /lib64/libc.so.6() [0x37da62ba4e]
[5] /lib64/libc.so.6::(null) + 0  [0x37da62bb10]
[6]
/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique::(null)
+ 0x24cc  [0x40818c]
[7] /lib64/libc.so.6::(null) + 0xfd  [0x37da61ed1d]
[8]
/work/.apps/unit/sqc_team/celera/wgs-8.3rc2/Linux-amd64/bin/markRepeatUnique()
[0x4083b9]

GDB:

Any comments or workarounds are very much appreciated. Thank you in advance.

Best regards,

Ryo Koyanagi

koy...@oi...
Okinawa Institute of Science and Technology, Japan