wtdbg2 killed after indexing kmers

[gchchung]

New here. Attempting to assemble a nematode genome ~100-200 Mbps, reads obtained using Nanopore. When I run

wtdbg2 -x ont -g 200m -i Dpachys_FAL80830_trimmed.fasta -fo trimmed_assembly_test

I get a kill message immediately after indexing kmers. Any ideas why this might be? (Output below)

--
-- total memory       30822548.0 kB
-- available          30509332.0 kB
-- 8 cores
-- Starting program: wtdbg2 -x ont -g 200m -i Dpachys_FAL80830_trimmed.fasta -fo trimmed_assembly_test
-- pid                      2014
-- date         Fri Aug  7 21:36:39 2020
--
[Fri Aug  7 21:36:39 2020] loading reads
1722266 reads
[Fri Aug  7 21:40:03 2020] filtering from 1722266 reads (>=5000 bp), 23163908045 bp. Try selecting 10000000000 bp
[Fri Aug  7 21:40:05 2020] Done, 415372 reads (>=5000 bp), 10000001024 bp, 39062438 bins
** PROC_STAT(0) **: real 205.650 sec, user 90.520 sec, sys 26.860 sec, maxrss 6387776.0 kB, maxvsize 6902196.0 kB
[Fri Aug  7 21:40:05 2020] Set --edge-cov to 3
KEY PARAMETERS: -k 15 -p 0 -K 1000.049988 -A -S 2.000000 -s 0.050000 -g 200000000 -X 50.000000 -e 3 -L 5000
[Fri Aug  7 21:40:05 2020] generating nodes, 4 threads
[Fri Aug  7 21:40:05 2020] indexing bins[(0,39062438)/39062438] (9999984128/22943717376 bp), 4 threads
[Fri Aug  7 21:40:05 2020] - scanning kmers (K15P0S2.00) from 39062438 bins
39062438 bins
********************** Kmer Frequency **********************

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**********************     1 - 201    **********************
Quatiles:
   10%   20%   30%   40%   50%   60%   70%   80%   90%   95%
     7    22    43    62    78   107   144   211   438   941
** PROC_STAT(0) **: real 544.633 sec, user 1420.220 sec, sys 52.810 sec, maxrss 11588868.0 kB, maxvsize 12176708.0 kB
[Fri Aug  7 21:45:44 2020] - high frequency kmer depth is set to 1000
[Fri Aug  7 21:45:44 2020] - Total kmers = 238277786
[Fri Aug  7 21:45:44 2020] - average kmer depth = 22
[Fri Aug  7 21:45:44 2020] - 37403133 low frequency kmers (<2)
[Fri Aug  7 21:45:44 2020] - 103311 high frequency kmers (>1000)
[Fri Aug  7 21:45:44 2020] - indexing 200771342 kmers, 4435196807 instances (at most)
0Killed

[ruanjue]

Should be out of memory.

[gchchung]

Thanks for the tip @ruanjue. Any way to limit the amount of memory wtdbg2 uses? (Not a big deal as I can run this with more memory.)

[ruanjue]

-S <val>, set the val to 4 or more. But will hurt the assembly.

[gchchung]

Sounds good. I'll give that a try! Thanks.