NumberFormatException in aggregate_statistics_post_rsrs analysis task

[gregsoos]

The analysis.wdl workflow calls the aggregate_statistics task from demultiplex.wdl as aggregate_statistics_post_rsrs. This task essentially runs the AggregateStatistics function from the adnascreen jar over the stats files created by the rsrs_chromosome_target_post task. However, if something unexpected is written to one of the stats files but the chromosome_target task still completes, this leads to a less traceable error in aggregate_statistics_post_rsrs.

For example, I had the following error in aggregate_statistics_post_rsrs:

java -Xmx1750m -jar 1327423679/adnascreen-1.11.6-SNAPSHOT.jar AggregateStatistics 1159663773/*.stats Exception in thread "main" java.lang.NumberFormatException: For input string: "[0.004s][warning][perf,memops] Cannot use file /tmp/hsperfdata_grs495/1925719 because it is locked by another process (errno = 11)" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Long.parseLong(Long.java:618) at java.base/java.lang.Long.valueOf(Long.java:974) at adnascreen.SampleSetsCounter.<init>(SampleSetsCounter.java:47) at adnascreen.AggregateStatistics.main(AggregateStatistics.java:33) at adnascreen.Driver.main(Driver.java:37)

Which stemmed from "[0.004s][warning][perf,memops] Cannot use file /tmp/hsperfdata_grs495/1925719 because it is locked by another process (errno = 11)" being written to one of the stats files during call-rsrs_chromosome_target_post.