aligmnet of mutli-fasta fie to reference genome

Question

[anna]

Hi, I want to check similarity of the draft genome (250 contigs in total) to the reference genome using BRIG. I made a run but it did not work. On terminal I had some complains in regard to java such as:

java.lang.IllegalArgumentException: Comparison method violates its general contract!
    at java.util.TimSort.mergeHi(TimSort.java:868)
    at java.util.TimSort.mergeAt(TimSort.java:485)
    at java.util.TimSort.mergeCollapse(TimSort.java:408)
    at java.util.TimSort.sort(TimSort.java:214)
    at java.util.TimSort.sort(TimSort.java:173)
    at java.util.Arrays.sort(Arrays.java:659)
    at brig.Main.reverseBlast(Main.java:206)
    at brig.Main.BlastMaster(Main.java:1494)
    at brig.Main.ParseBlast(Main.java:1352)
    at brig.Three2.compute(Three2.java:337)
    at brig.Three2.access$300(Three2.java:33)
    at brig.Three2$4.run(Three2.java:234)

I made a test where I selected one and two contigs and ran that against reference. That worked quite ok. However, when I selected more than 10 contigs I see the same message as in case of 250 contigs. I will appreciate any suggestions.

[apelin20]

Run it on batches of 10 contigs... 1-10, 11-20, 21-30... see where the error is. Clearly it's one of the contigs, or maybe amount of contigs.

Answer 1

[Pierre Lindenbaum]

This is a programming error. http://stackoverflow.com/questions/11441666

There is nothing you can do unless modifying the java code.

Answer 2

[Rajesh Detroja]

You can use MUMmer tool (http://mummer.sourceforge.net/) for Genome Alignment.

Answer 3

[kapil.joshi036]

if your data is rna the use bowtie2 or even try shrimp to do it