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Fast and frugal disk based k-mer counter
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KMC froze at Stage 1: 2% #242

Open zhangrengang opened 1 month ago

zhangrengang commented 1 month ago

When I count kmers for a large BAM file (586 Gb), KMC froze with CPU% = 0. The following is the log:

+ kmc -fbam -k19 -t32 -m256 -ci1 -cs100000000 -cx1000000000 @seq.list BPS02_19 /dev/shm/kmc3041468.BPS02_19
***********************************************************************************************************************************************************************************
Stage 1: 2%

The KMC version: ver. 3.2.4 (2024-02-09)