[mira_talk] problem with convert_project -t hsnp
- From: Davide Sassera <davide.sassera@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 22 Jun 2012 10:50:38 +0200
Hi Bastien, Hi guys,
I mapped solexa reads from 2 strains (K26 and K28) on a draft genome
(K30 -458 contigs) using the following command:
mira --project=doublemap --job=mapping,genome,accurate,solexa
-FN:sdi=K26_K28_4mill.straindata:bbin=K30_23maggio.gbk -AS:nop=1
-SB:lsd=yes:bsn=K30:bft=gbf:bbq=30 SOLEXA_SETTINGS
-FN:fqi=K26_K28_4mill.fastq -GE:uti=no:tismin=150:tismax=450
>&log_assembly.txt
I got my results, then, following the manual like a bible, I attempted
convert_project -f caf -t asnp doublemap_out.caf doublemap_out
Which worked, I will analyze the results now
and
convert_project -f caf -t hsnp doublemap_out.caf doublemap_out
Which did not work, giving the error below.
Any idea on what happened?
Seeing strain 1: "K28"
Seeing strain 2: "K26"
Seeing strain 3: "K30"
Generated 3 unique strain ids for 1314 reads.
Saving SNP surroundings as HTML to file:
doublemap_out_info_snpenvironment.html
Localtime: Fri Jun 22 10:01:28 2012
Generated 664 unique template ids for 755 valid reads.
Localtime: Fri Jun 22 10:01:28 2012
Seeing strain 1: "K28"
Seeing strain 2: "K26"
Seeing strain 3: "K30"
Generated 3 unique strain ids for 755 reads.
Saving SNP surroundings as HTML to file:
doublemap_out_info_snpenvironment.html
Localtime: Fri Jun 22 10:01:28 2012
Generated 1691 unique template ids for 1843 valid reads.
Localtime: Fri Jun 22 10:01:28 2012
Seeing strain 1: "K28"
Seeing strain 2: "K26"
Seeing strain 3: "K30"
Generated 3 unique strain ids for 1843 reads.
Saving SNP surroundings as HTML to file:
doublemap_out_info_snpenvironment.html
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"Cont5.7: readpos (4294967293) >= size of read (13193)?"
->Thrown: int32 Read::getLowerNonGapAdjustmentPosOfReadPos(const uint32
position) const
->Caught: Error while creating CAF-Object.
Aborting process, 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.
If reporting, please do not delete the log and checkpoint directories,
there may
be files in them which could be needed to find the problem.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD:
/media/sdb/home/banana/Kleb_doublemapping/doublemap_assembly/doublemap_d_results
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
--
Davide Sassera
Dipartimento di Scienze Veterinarie e Patologia Animale
Via Celoria 10 - 20133 Milano - Italy
tel: +390250318094
fax: +390250318095
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