bitArray-v1.H:86 problem when running the pipeline

[mike-bioinfo]

Hi everyone,

I have some issues running the pipeline in a 600mb genome and I would like to know if someone could help me. Here is my log with the error that I ran into.

Opening outputs: '-' setBit()-- ERROR: position=305 > maximum available=0 meryl-lookup: utility/src/bits/bitArray-v1.H:86: void merylutil::bits::v1::bitArray::setBit(uint64, bool): Assertion `position < _maxBitAvail' failed.

Failed with 'Aborted'; backtrace (libbacktrace): utility/src/system/system-stackTrace-v1.C::82 in _Z17AS_UTL_catchCrashiP9siginfo_tPv() (null)::0 in (null)() (null)::0 in (null)() (null)::0 in (null)() (null)::0 in (null)() (null)::0 in (null)() utility/src/bits/bitArray-v1.H::86 in _ZN9merylutil4bits2v18bitArray6setBitEmb() meryl-lookup/dump.C::128 in processSequence() utility/src/system/sweatShop-v1.C::308 in _ZN9sweatShop6workerEP15sweatShopWorker() (null)::0 in (null)() (null)::0 in (null)() (null)::0 in (null)() /mnt/bin/merqury/merqury_v1.3//eval/spectra-cn.sh: line 71: 37401 Aborted (core dumped) meryl-lookup -bed -sequence $asm_fa -mers ${asm}.0.meryl > ${asm}_only.bed

Any feedback would be very appreciated.

Cheers, Mike.

[brianwalenz]

That seems to be the same as in https://github.com/marbl/merqury/issues/98. The resolution there was to compile meryl from either the master or v1.4-maintenance branch (both have the bugfix). Holler if you need help doing that.