void segmentGraph aborted

[srajedwin]

I attempt to identify the variants in our samples using squid. I aligned the reads using STAR 2-pass including chimeric bam.

Squid run was aborted after build nodes, finish seeding with the following errors:

[Tue Oct 23 14:52:31 2018] Start reading bam file. [Tue Oct 23 15:31:14 2018] Finish sorting Chimeric bam reads. [Tue Oct 23 15:45:26 2018] Finish removing PCR duplicates. [Tue Oct 23 15:49:56 2018] Building nodes. |bamdiscordant|=331264 [Tue Oct 23 15:50:05 2018] Building nodes, finish seeding.

squid: src/SegmentGraph.cpp:662: void SegmentGraph_t::BuildNode_STAR(const std::vector&, SBamrecord_t&, std::string): Assertion `vNodes[i].Length>0 && vNodes[i].Position+vNodes[i].Length<=RefLength[vNodes[i].Chr]' failed. /var/spool/pbs/mom_priv/jobs/7784253.wlm01.SC: line 36: 19875 Aborted squid -b PT_10_S3_L001Aligned.toTranscriptome.out.bam -c PT_10_S3_L002Aligned.sortedByCoord.out.bam -o PT_10_S3_L001_squid -G 1 -CO 1

Could you please suggest me a fix