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bioinfologics / w2rap-contigger

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.
http://bioinfologics.github.io/the-w2rap-contigger/
MIT License
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Step 3 crash #50

Closed mlcossette9224 closed 3 years ago

mlcossette9224 commented 3 years ago

I am getting the following error on step 3

--== Step 3: Repathing to second (large K) graph ==-- Tue Mar 02 13:15:06 2021: beginning repathing 31790560 edges from K=60 to K2=64 Tue Mar 02 13:15:06 2021: constructing places from 1308014986 paths Tue Mar 02 13:15:12 2021: 1265069099 / 1308014986 reads pathed, 173319806 spanning junctions Tue Mar 02 13:20:49 2021: sorting 1264197670 places Tue Mar 02 14:03:45 2021: 77032864 unique places Tue Mar 02 14:03:45 2021: building all Tue Mar 02 14:08:44 2021: calling LongReadsToPaths Fatal error (pid=16780) at Tue Mar 02 14:08:44 2021: Illegal value 64 for K in BigK dispatcher.

What should I do?

bjclavijo commented 3 years ago

You seem to be using 64 as the value for large_K. Allowed values are: {20, 24, 28, 32, 40, 48, 60, 72, 80, 84, 88, 96, 100, 108, 116, 128, 136, 144, 152, 160, 168, 172, 180, 188, 196, 200, 208, 216, 224, 232, 240, 260, 280, 300, 320, 368, 400, 500, 544, 640, 720, 1000, 1200, 1600, 2000, 4000, 10000}

Keep in mind you want that value to be larger than small_k and smaller than your read size.

Best,

bj