Closed LindseyBohr closed 5 years ago
JosephCrispell
commented
5 years ago Hi Lindsay,
Thanks very much for using the tool and sorry about the bug!
HomoplasyFinder should be able to account for gaps in the alignment, so I don't think that can be the issue. Would it be possible for you to send me a newick tree file and nucleotide fasta file that I can replicate the problem on?
Thanks again for using the tool!
Joe
JosephCrispell
commented
5 years ago Hi Lindsay,
To hopefully make identifying your issue a little easier, I have added some additional error messaging into HomoplasyFinder. Would it be possible for you to download the latest version of the HomoplasyFinder.jar from here and give it a go?
I also slightly edited the code to account for lowercase characters in the alignment, in case that was causing your problem.
Thanks!
Joe
LindseyBohr
commented
5 years ago That worked! I did get this error first when running it:
ERROR!! Unrecognised character (?) in nucleotide alignment at position: 71
but after changing them all to dashes instead, it ran perfectly.
Thank you!
Lindsey
JosephCrispell
commented
5 years ago Hi Lindsey,
That is great! Thanks very much for pointing the bug out and thank you for using HomoplasyFinder.
Joe
How are gaps in the aln handled?
Running HomoplasyFinder.jar at the command line on ~74 closely related isolates and getting this error:
Exception in thread "main" java.lang.NullPointerException at homoplasyFinder.ConsistencyIndex.comparePossibleNucleotidesOfTwoSubNodes(ConsistencyIndex.java:444) at homoplasyFinder.ConsistencyIndex.getPossibleStateForInternalNodeFromPossibleStatesOfSubNodes(ConsistencyIndex.java:421) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:407) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.identifyPossibleStatesForInternalNode(ConsistencyIndex.java:394) at homoplasyFinder.ConsistencyIndex.calculateMinimumNumberOfChangesOnPhylogeny(ConsistencyIndex.java:372) at homoplasyFinder.ConsistencyIndex.calculateConsistencyIndexForEachSiteOnPhylogeny(ConsistencyIndex.java:274) at homoplasyFinder.ConsistencyIndex.<init>(ConsistencyIndex.java:110) at homoplasyFinder.HomoplasyFinder.main(HomoplasyFinder.java:26)I'm wondering if it's because I have gaps in my data denoted with "-"