[mira_talk] Bug report 3.9.10
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 13 Mar 2013 11:04:14 -0400
Hi Bastien,
I just got this error message:
A file named 'addReaderror_REPLAY_do_not_delete.log' has been written
to the working directory. Please send it to the author to get that bug fixed!
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"WARNING/ERROR: contig did not put refid into affected reads. Please file a bug
report to
https://sourceforge.net/apps/trac/mira-assembler/
and please send a mail to
mira_talk@xxxxxxxxxxxxx
"
->Thrown: void Contig::addRead(vector<Align> & aligncache, const
AlignedDualSeqFacts * initialadsf, int32 refid, int32 newid, int32
direction_frnid, errorstatus_t & errstat)
->Caught: void Contig::addRead(vector<Align> & aligncache, const
AlignedDualSeqFacts * initialadsf, int32 refid, int32 newid, int32
direction_frnid, errorstatus_t & errstat)
Aborting process, probably due to an internal error.
---
It occurred during Pass 1 / 5
The assembly was the following:
I reference mapped a small eukaryote genome(10 megabase) to a closely related
genome. I then grabbed the unmapped reads from the paired 454 reads and the
unpaired 454 reads to separate read files, and performed a de novo assembly
from these unmapped reads, of which there were 1890039 (248877164 bases) before
all the clipping routines started.
I'll send you the addReaderror_REPLAY_do_not_delete.log file back channel, and
I'll not delete the working directory yet, in case you need more.
Is it worth re-trying with 3.9.4 or even 3.4?
cheers,
John
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