java.lang.NullPointerException error in IGVtools when trying to Find Motif
0
0
Entering edit mode
5.2 years ago
michael.nagle ▴ 100

I am running the latest version of IGVtools and have several .fa files loaded. I am now trying to locate a particular motif in these files. I start with Tools -> Find Motif, enter the sequence, then get this error. How should I go about resolving this? Thanks

INFO [2016-07-06 10:57:15,174] [MessageUtils.java:74] Error loading features for interval: scaffold_4:17206330-24417620
java.lang.NullPointerException ERROR [2016-07-06 10:57:29,139] [FeatureTrack.java:925] Error loading features for interval: scaffold_4:17206330-24417620
java.lang.NullPointerException java.lang.NullPointerException at htsjdk.samtools.util.SequenceUtil.reverseComplement(SequenceUtil.java:594) at org.broad.igv.tools.motiffinder.MotifFinderSource.getMatcher(MotifFinderSource.java:116) at org.broad.igv.tools.motiffinder.MotifFinderSource.searchSingleStrand(MotifFinderSource.java:99) at org.broad.igv.tools.motiffinder.MotifFinderSource.search(MotifFinderSource.java:140) at org.broad.igv.tools.motiffinder.MotifFinderSource.getFeatures(MotifFinderSource.java:156) at org.broad.igv.feature.CachingFeatureSource.queryRaw(CachingFeatureSource.java:68) at org.broad.igv.feature.AbstractCacher.loadTiles(AbstractCacher.java:198) at org.broad.igv.feature.AbstractCacher.getBins(AbstractCacher.java:172) at org.broad.igv.feature.AbstractCacher.queryCached(AbstractCacher.java:102) at org.broad.igv.feature.CachingFeatureSource.getFeatures(CachingFeatureSource.java:73) at org.broad.igv.track.FeatureTrack$1.run(FeatureTrack.java:903) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

igvtools java • 2.0k views
ADD COMMENT
0
Entering edit mode

please post this bug on https://github.com/igvteam/igv/issues

ADD REPLY

Login before adding your answer.

Traffic: 1026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6