Sanity check failures in AssemblyFactory

[mpinese]

Hi, thanks for turning around that THREADS fix so quickly. I've been testing GRIDSS on WGS of normal blood, and preliminary results are looking very nice. I am however getting some sanity check failures:

INFO    2017-03-03 20:18:39     AssemblyEvidenceSource  Starting assembly on chunk 24 (1:240000001-249250621)
INFO    2017-03-03 20:19:41     AssemblyEvidenceSource  Completed assembly on chunk 17 (1:170000001-180000000) in 3424s (57.07 min)
INFO    2017-03-03 20:19:41     SAMFileUtil     Sorting /jobfs/local/2814812.r-man2/GRIDSS/test_run.gridss.assembly.bam.gridss.working/gridss.tmp.test_run.gridss.assembly.bam.assembly.chunk17.bam
INFO    2017-03-03 20:19:41     AssemblyEvidenceSource  Starting assembly on chunk 25 (2:1-10000000)
WARNING 2017-03-03 20:35:04     AssemblyFactory Negative deletions not supported by SAM specs. Breakpoint assembly has been converted to breakend. Sanity check failure: this should not be possible for positional assembly.
WARNING 2017-03-03 20:36:05     AssemblyFactory Negative deletions not supported by SAM specs. Breakpoint assembly has been converted to breakend. Sanity check failure: this should not be possible for positional assembly.
INFO    2017-03-03 20:37:05     AssemblyEvidenceSource  Completed assembly on chunk 18 (1:180000001-190000000) in 3531s (58.86 min)
INFO    2017-03-03 20:37:05     SAMFileUtil     Sorting /jobfs/local/2814812.r-man2/GRIDSS/test_run.gridss.assembly.bam.gridss.working/gridss.tmp.test_run.gridss.assembly.bam.assembly.chunk18.bam
INFO    2017-03-03 20:37:05     AssemblyEvidenceSource  Starting assembly on chunk 26 (2:10000001-20000000)

Is this anything to be worried about?

[d-cameron]

Is this anything to be worried about?

I wouldn't think so. All instance of these that I've looked at were misassemblies of low complexity sequence for which the assembly contigs were filtered in a later step anyway.

[mpinese]

Good to know, thanks.