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loneknightpy / idba

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idba_ud memory problem and crash (killed) #10

Open tallnuttcsiro opened 8 years ago

tallnuttcsiro commented 8 years ago

Using 1.1.2 and still get this problem. I have itnerleaved fasta file of 300bp reads, so have to use "-l" option in 1.1.2. Get the same error with any kmer length but 124 bp shown. The program uses all memory (80GB), then swap disks until it is 'killed' as shown (not by me). Thanks for any help. Can't use idba at all until this is fixed.

idba_ud -l ~/d/031/reads/int_fasta/2937_WT.fasta -o ~/d/031/idba/2937_WT --num_threads 29 --mink 124 --maxk 124 --step 0 number of threads 29 reads 0 long reads 1963614 extra reads 0 read_length 0 kmer 124 kmers 3906398 3897506 merge bubble 92 Killed

tallnuttcsiro commented 8 years ago

Does anyone know if IDBA is still being supported? This seems to be a fairly leathal bug. Is anyone else still getting it?

I'm using gcc version 4.7.2, Debian 4.7.2-5.

Thanks