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Find all significant local alignments between reads
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LAsort Issue when called from daligner #94

Open BradleyRan opened 4 years ago

BradleyRan commented 4 years ago

I am seeing current version of LAsort failing when called from daligner. As a workaround, I have been using an older version of LAsort.

ie (dentistenv) [randy.bradley@ceres18-mem-2 workdir]$ daligner -I -l500 -e0.980100 -M25 '-T8' -P/project/cattle_genome_assemblies/dentist-test/workdir scaffolds_FINAL.4 scaffolds_FINAL.5

daligner2.0: Command Failed: LAsort /project/cattle_genome_assemblies/dentist-test/workdir/daligner.96981/scaffolds_FINAL.4.scaffolds_FINAL.5.N@

BradleyRan commented 4 years ago

I ran the job again with the "-v" option. Attached are 2 log files. It looks like the current version failed at scaffolds_FINAL.2.scaffolds_FINAL.2.N1: 96,674 records 5,357,506 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N2: 109,181 records 4,219,086 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N3: 0 records 12 trace bytes

While the older LSsort continued on with scaffolds_FINAL.2.scaffolds_FINAL.2.N1: 96,674 records 5,357,506 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N2: 109,181 records 4,219,086 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N3: 0 records 12 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N4: 63,541 records 3,229,604 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N5: 93,697 records 2,789,010 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N6: 113,950 records 3,391,542 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N7: 0 records 12 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N8: 49,470 records 1,476,054 trace bytes Merging 8 files totaling 526,513 records failed-self-alignment.2.2.log successful-self-alignment.2.2.log

thegenemyers commented 4 years ago

Basically some kind of edge-case problem, the file LAsort failed on had no, i.e. 0, overlaps in it.

I've just checked in a new version that should fix this problem. Please let me know if not.

Best,  Gene

On 7/17/20, 1:15 AM, BradleyRan wrote:

I ran the job again with the "-v" option. Attached are 2 log files. It looks like the current version failed at scaffolds_FINAL.2.scaffolds_FINAL.2.N1: 96,674 records 5,357,506 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N2: 109,181 records 4,219,086 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N3: 0 records 12 trace bytes While the older LSsort continued on with scaffolds_FINAL.2.scaffolds_FINAL.2.N1: 96,674 records 5,357,506 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N2: 109,181 records 4,219,086 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N3: 0 records 12 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N4: 63,541 records 3,229,604 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N5: 93,697 records 2,789,010 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N6: 113,950 records 3,391,542 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N7: 0 records 12 trace bytes scaffolds_FINAL.2.scaffolds_FINAL.2.N8: 49,470 records 1,476,054 trace bytes Merging 8 files totaling 526,513 records failed-self-alignment.2.2.log successful-self-alignment.2.2.log

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