[mira_talk] Re: [mira-assembler] #5: mapping error on 3rd incremental step.
- From: "William C. Curtiss" <wcurtiss@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 5 Jan 2010 10:18:51 -0800 (PST)
I am looking for suggestions to assemble a plant genome of about 400,000,000
bases.
I
am atempting to use an incremental approach with an initial denovo
assembly of 100,000 reads followed by mapping of successive 100,000
reads (for a total of 2,000,000 reads). The denovo assembly and the
first 4 mapping runs were successful but the next mapping run fails. I
have filed a ticket as suggested.
While a resource limit would
seem the most likely, the command "free" always showed free RAM and
little swap being used. The machine is running RedHat Linux 64bit 32 GB RAM and
32 GB swap with 2 quad core cpus.
The command line is:
nohup nice time \
mira \
-fasta \
-project=$pname \
-GENERAL:number_of_threads=1 \
-STRAIN/BACKBONE:backbone_filetype=caf:abnc=yes \
--job=mapping,genome,draft,sanger SANGER_SETTINGS \
-LOADREADS:readnaming_scheme=TIGR \
-CLIPPING:bad_stretch_quality_clip=yes \
-CONTIG:min_groupqual_for_rmb_tagging=30 \
2>&1 | tee -a $log &
Below are the last few lines from the log file showing the error mesage:
1516: * -1 50 f: invld #0 r; invld #0
1517: * -1 50 f: invld #0 r; invld #0
1518: * -1 50 f: invld #0 r; invld #0
1519: * -1 45 f: invld #0 r; invld #0
1520: * -1 43 f: invld #0 r; invld #0
1521: * -1 43 f: invld #0 r; invld #0
1522: * -1 43 f: invld #0 r; invld #0
1523: * -1 43 f: invld #0 r; invld #0
Exiting.
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-
assembler/
"####204194####: to (4294967295) >= len of sequence (1524) ?"
->Thrown: void Read::addTag(uint32 from, uint32 to, const string &
identifier, const string & comment)
->Caught: void Assembly::transferContigReadTagsToReadpool(const Contig &
con, const list<Contig>::const_iterator bbContigI)
Program aborted, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
Command terminated by signal 6
2026.51user 275.50system 36:13.07elapsed 105%CPU (0avgtext+0avgdata
0maxresident)k
0inputs+0outputs (49major+5556330minor)pagefaults 0swaps
Mon Jan 4 17:08:03 CST 2010
I am probably not looking at the right parts of the output and documentation.
Any suggestions would be great.
Thanks
Bill Curtiss
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