I left my first Contig Mover graphical run going overnight on a Windows PC,
aligning ~10,000 large contigs from one new microbial eukaryotic genome
project, to one finished reference genome from a closely related species,
consisting of 15 chromosomes; the reference genome is ~25Mb . The 15 full
genbank records for the chromosomes were in one .gbk file, the 10,000 contigs
in a single multi-fasta .fna file.
MCM appears to have done 7 alignments in total. They're all on the desktop.
The output folder contains these dirs and files:
Contigs (directory)
alignment7
alignment7.backbone
alignment7.bbcols
alignment7.guide_tree
cyno_LargeContigs.fna.fas.sslist
cyno_LargeContigs.fna_contigs.tab
cyno_LargeContigs.fna.fas
v_genome.gbk.sslist
v_genome.gbk
The console shows this at the end of the run:
done.
Working set size: 706 Mb
Pagefile usage : 503.
Root alignment has 52 superintervals
Root alignment length : 32593453
Organisms have 40.4 % GC
Completed without error
Shown
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Exception in thread "Thread-39" java.lang.Error: Inconsistency error
at org.gel.mauve.tree.GISTree._splay(Unknown Source)
at org.gel.mauve.tree.GISTree.splay(Unknown Source)
at org.gel.mauve.tree.GISTree.find_seqIndex(Unknown Source)
at org.gel.mauve.tree.GISTree.seqPosToColumn(Unknown Source)
at org.gel.mauve.XMFAAlignment.getLCBAndColumn(Unknown Source)
at org.gel.mauve.backbone.BackboneList.getNextBackbone(Unknown Source)
at org.gel.mauve.contigs.ContigGrouper$ContigGroup.getNonEmpty(Unknown Source)
at org.gel.mauve.contigs.ContigGrouper$ContigGroup.<init>(Unknown Source)
at org.gel.mauve.contigs.ContigGrouper.getContigGroup(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.removeBadLCBs(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.adjustLCBs(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.process(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.fixContixs(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initModelData(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer$ReordererMauveFrame$1.run(Unknown
Source)
at java.lang.Thread.run(Unknown Source)
Should I be worried?
(Btw, the 'whitespace' message , presumably referring to whitespace the
reference .gbk file, occurred multiple times during the run. There also
appears to be another, different set of java errors after the 3rd alignment. )
---
Steven Sullivan, Ph.D.
Bioinformatics Analyst
Dept. of Medical Parasitology
New York University Langone Medical Center
PH: (212) 263-4378
---
Steven Sullivan, Ph.D.
Bioinformatics Analyst
Dept. of Medical Parasitology
New York University Langone Medical Center
PH: (212) 263-4378
</PRE>
<html>
<body>
------------------------------------------------------------<br />
This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain information that is proprietary,
confidential, and exempt from disclosure under applicable law. Any unauthorized
review, use, disclosure, or distribution is prohibited. If you have received
this email in error please notify the sender by return email and delete the
original message. Please note, the recipient should check this email and any
attachments for the presence of viruses. The organization accepts no liability
for any damage caused by any virus transmitted by this email.<br />
=================================
</body>
</html>
<PRE>
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
