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v1.4 segfault consensus #174

@ptrebert

Description

@ptrebert

Hi,
I have a single case of a segfault in the consensus phase:

  21699 Failed with 'Aborted'; backtrace (libbacktrace):
  21700  - ALIGNED 0.0238 at    133292-142920   
  21701 ERROR:  alignment from 133293 to 142920, but tiglen is only 132087
  21702 utgcns: utgcns/unitigConsensus.C:867: bool alignEdLib(dagAlignment&, tgPosition&, char*, uint32, char*, uint32, double, bool): Assertion `aln.end <= tiglen' failed.
  21703 
  21704 Failed with 'Aborted'; backtrace (libbacktrace):
  21705 
  21706 Failed with 'Segmentation fault'; backtrace (libbacktrace):
  21707 ./packages/part026.sh: line 19: 135788 Segmentation fault      /[...]/verkko/wd/.snakemake/conda/c410c39ac1cf6bea6ae75
  21707 0999a5ce20f_/lib/verkko/bin/utgcns -V -V -V -threads 8 -import ../7-consensus/packages/part026.cnspack -A ../7-consensus/packages/part026.fasta.WORKING -C 2 -norealign -max
  21707 coverage 50 -e 0.05 -em 0.20 -EM 0 -l 3000 -edlib
  21708 
  21709 Consensus did not finish successfully, exit code 0.

It's v1.4 plus two bug fixes (3119b39 and 4f6a54e). As a side note, the overall run was registered by Snakemake as having failed, despite the weird did not finish successfully, exit code 0.

Best,
Peter

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