[mira_talk] Mapping segmentation fault v3.9.5
- From: "Jackie Lighten" <jackie.lighten@xxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 31 Oct 2012 15:33:54 -0300
Hi,
I get a core dump when Mira attempts to write contigs (see below for
manifest file inputs and where the dump takes place)
I am running on a virtual machine that has over 20GB RAM and 4 threads
allocated.
Any idea how to remedy this?
The only log file I could find was in the temp folder, named
"miralog.noqualities", and was empty.
Many thanks in advance
Manifest file:
project = cDNAvsReference
job = mapping,est,accurate
parameters = -GE:number_of_threads=4 \
COMMON_SETTINGS -SB:abnc=yes \
-OUT:ota=on \
454_SETTINGS -CL:qc=no:cpat=1 \
-AS::enforce_presence_of_qualities=no \
readgroup=cDNA
data=cDNA_in.454.fasta
technology=454
readgroup=backbone
data= backbone_in.fna
technology=454
as_reference
Error:
"
Sorting confirmed overlaps (this may take a while) ... done.
Localtime: Wed Oct 31 11:19:08 2012
Generating clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Sorting clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] Localtime: Wed Oct 31 11:19:09 2012
Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Writing unclustered reads ... done.
Localtime: Wed Oct 31 11:19:10 2012
BFC: 1 1
overlapcompressstepping: 100000
nextoverlapcompress: 100000
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Done. 0 reads moved to debris.
bfc 1
Localtime: Wed Oct 31 11:19:11 2012
Timing BFC unused: 1082
CUnused: 1116522
TUnused: 1116522
AS_used_ids.size(): 1264803
bfc 2
Timing BFC prelim1: 19
bfc 3
bfc 4
Timing BFC discard con: 7
bfc 5
bfc 6/0
Timing BFC copy bbcon: 184
Timing BFC bbsetup remain: 18
bfc 7/0
Building new contig 1 from backbone gi|48691682|gb|CO049346.1|CO049346_bb
Localtime: Wed Oct 31 11:19:11 2012
Unused reads: 1116522
bfc 8/0
assemblymode_mapping: 0
use general pathfinder: 0
no bfccp3
Timing priv_initialiseLowerBoundOEdges: 206000
Segmentation fault (core dumped)
mgpl@ubuntu:~/Desktop/mira3.9.5/bin$ "
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