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thegenemyers / DALIGNER

Find all significant local alignments between reads
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LAshow: Segmentation fault #71

Closed pb-cdunn closed 6 years ago

pb-cdunn commented 6 years ago

I've double-checked that this happens with your version too, latest code.

LAshow -ac comp raw_reads.comp.las
/bin/sh: line 1: 30550 Segmentation fault      (core dumped)

-c is fine, and sans flag is fine. Only -a crashes. It seems to die somewhere in a Compute_Trace_Points().

gm.tgz has everything you need. But if you'd rather have original fastas, just let me know, Gene.

thegenemyers commented 6 years ago

Actually, LAshow is fine. The call should be

'LAshow -ac raw_reads comp raw_reads.comp.las'

You called HPC.daligner with two different databases, 'raw_reads' and 'comp', so to list the alignment LAshow needs to be given each database so it can look up the reads (note that LAcheck in the script does this). When you call it with only one database, comp, it assumes the A and B reads both come from comp and looks them up there. Since the A reads come from raw_reads, Compute_Trace is being called with the wrong A read, and so it is comparing some random A to the B-read, so alignment can fail in any number of ways since the trace points are no longer valid.

It was a pain in the ass, but I added checks to Compute trace, so that it reports that the trace is invalid (either because it goes off the end of a read, or because it can't find an alignment with the known difference between two trace points). So now you get an error message about trace points either being out of bounds or the alignment not making any sense, with the tip that the source DB's may not be specified corrrectly.

-- Gene

On 11/6/17, 3:44 PM, Christopher Dunn wrote:

I've double-checked that this happens with your version too, latest code.

LAshow -ac comp raw_reads.comp.las /bin/sh: line 1: 30550 Segmentation fault (core dumped)

|-c| is fine, and sans flag is fine. Only |-a| crashes. It seems to die somewhere in a |Compute_Trace_Points()|.

|gm.tgz| has everything you need. But if you'd rather have original fastas, just let me know, Gene.

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