error when running Mauve to re-order contigs
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18 months ago
zhangdengwei ▴ 150

Hi all,

I am using Mauve to re-order the assembled contigs, some sample worked well but some failed, and I got the following error

root alignment has 57 superintervals root alignment length: 5472933 Organisms have 50.8% GC Completed without error. Alignment complete! made reorder frame shown initing data in process. . . Exception in thread "Thread-52" 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.fixContigs(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(Thread.java:745)

Is there anyone who know what happened? Any suggestions would be greatly appreciated!!!

comparative genome Mauve genome assembly • 518 views
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I am facing the same issue. Have you already solved it? Thanks a lot.

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no, I still have no idea.

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