I have been having this issue while running SQUID to obtain transcriptomic structural variants from RNASEQ data. This is the error that I have been receiving.
[Thu Aug 12 00:29:10 2021] Start reading bam file.
[Thu Aug 12 00:29:34 2021] Finish sorting Chimeric bam reads.
[Thu Aug 12 00:29:35 2021] Finish removing PCR duplicates.
[Thu Aug 12 00:29:37 2021] Building nodes. |bamdiscordant|=805622
[Thu Aug 12 00:30:07 2021] Building nodes, finish seeding.
squid: src/SegmentGraph.cpp:662: void SegmentGraph_t::BuildNode_STAR(const std::vector<int>&, SBamrecord_t&, std::string): Assertion `vNodes[i].Length>0 && vNodes[i].Position+vNodes[i].Length<=RefLength[vNodes[i].Chr]' failed.
Aborted (core dumped)
I tried to contact the professor in-charge of this tool with the exact same query, who then forwarded my email to one of the developers of this tool. This was their response email that I received.
Extremely disheartened by the response and unacceptable from the developers who made this tool to be used by the community.
I have been having this issue while running SQUID to obtain transcriptomic structural variants from RNASEQ data. This is the error that I have been receiving.
I ran the code with the following command
I tried to contact the professor in-charge of this tool with the exact same query, who then forwarded my email to one of the developers of this tool. This was their response email that I received. Extremely disheartened by the response and unacceptable from the developers who made this tool to be used by the community.