I'm having a problem with genome music. When I use
genome music bmr calcBmr with only 1
bmr-group (default) I do not seem to have a problem. However, when I set the the bmr-group to 10, then I often get the following error. Note, I have 300+k mutations and 3,000 samples total so it doesn't seem like it should be because all the mutations were skipped.
Finished Parsing the MAF file to classify mutations Skipped 86999 mutation(s) that are classified as Silent Skipped 1322 mutation(s) that are outside any ROIs Skipped 272 mutation(s) that have unrecognized gene names Use of uninitialized value $centroids in division (/) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 608. ERROR: Illegal division by zero at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 608.
Does anybody know what might be wrong? Can the number of groups just not go that high because it becomes too sparse? I'm also running two calcBmr's in parallel, so this also could be a problem (genome music seems to make heavy usage of the /tmp directory).