Error occurs when assembling contigs for k=???

[yifangt]

Hello,
When I tried to run megahit to do assembly, there was always error:
Error occurs when assembling contigs for k=25
[Exit code -4]
The kmer setting is the --k-min value, and I have tried different odd number from 15 ~ 25. None worked!
I checked the log file, which seems fine to read in all the reads, and parsed
My compiling went well, as no error or warning displayed. Use of the compiled and binary for both v0.2.1 and v0.3.0beta gave same error. See following log file:

MEGAHIT 0.3.0-beta
--- [Fri Jun 19 16:01:28 2015] Start assembly. Number of CPU threads 12 ---
--- [Fri Jun 19 16:01:28 2015] k list: 25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119,121,123 ---
--- [Fri Jun 19 16:01:28 2015] Extracting solid (k+1)-mers for k = 25 ---
cmd: /home/yifang/download-software/megahit_v0.3.0-beta_Linux_CUDA6.5_sm30/megahit_sdbg_build count -k 25 -m 2 --host_mem 128699280384 --mem_flag 1 --gpu_mem 0 --output_prefix S03/tmp/k25 --num_cpu_threads 12 --num_output_threads 4 --read_lib_file S03/tmp/reads.lib
[sdbg_builder.cpp : 101] Host memory to be used: 128699280384
[sdbg_builder.cpp : 102] Number CPU threads: 12
[cx1.h : 313] Preparing data...
[cx1_kmer_count.cpp : 101] 414255 reads, 245 max read length
[cx1.h : 320] Preparing data... Done. Time elapsed: 0.6206
[cx1.h : 327] Preparing partitions and initialing global data...
[cx1_kmer_count.cpp : 185] 2 words per substring, 3 words per edge
[cx1_kmer_count.cpp : 218] Memory for reads: 23971940
[cx1_kmer_count.cpp : 219] max # lv.1 items = 9636690
[cx1_kmer_count.cpp : 220] max # lv.2 items = 2097152
[cx1.h : 339] Preparing partitions and initialing global data... Done. Time elapsed: 0.1014
[cx1.h : 345] Start main loop...
[cx1.h : 366] Lv1 scanning from bucket 0 to 3127
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1263
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.5203
[cx1.h : 366] Lv1 scanning from bucket 3127 to 7636
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1240
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.5040
[cx1.h : 366] Lv1 scanning from bucket 7636 to 12575
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1198
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.5035
[cx1.h : 366] Lv1 scanning from bucket 12575 to 19039
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1209
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.5023
[cx1.h : 366] Lv1 scanning from bucket 19039 to 27609
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1221
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.4988
[cx1.h : 366] Lv1 scanning from bucket 27609 to 35970
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1223
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.5012
[cx1.h : 366] Lv1 scanning from bucket 35970 to 50072
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1252
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.4976
[cx1.h : 366] Lv1 scanning from bucket 50072 to 65536
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1154
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.2479
[cx1.h : 450] Main loop done. Time elapsed: 4.7557
[cx1.h : 456] Postprocessing...
[cx1_kmer_count.cpp : 636] Total number of candidate reads: 1414(3176)
[cx1_kmer_count.cpp : 646] Total number of solid edges: 273854
[cx1_kmer_count.cpp : 657] Output reads to binary file...
[cx1.h : 464] Postprocess done. Time elapsed: 0.2201
[utils.h : 114] Real: 5.7013 user: 40.9000 sys: 3.0360 maxrss: 203620
--- [Fri Jun 19 16:01:34 2015] Building graph for k = 25 ---
/home/yifang/download-software/megahit_v0.3.0-beta_Linux_CUDA6.5_sm30/megahit_sdbg_build seq2sdbg --host_mem 128699280384 --mem_flag 1 --gpu_mem 0 --output_prefix S03/tmp/k25 --num_cpu_threads 12 -k 25 --kmer_from 25 --num_edge_files 4 --input_prefix S03/tmp/k25 --need_mercy
[sdbg_builder.cpp : 310] Host memory to be used: 128699280384
[sdbg_builder.cpp : 311] Number CPU threads: 12
[cx1.h : 313] Preparing data...
[cx1_seq2sdbg.cpp : 383] Adding mercy edges...
[cx1_seq2sdbg.cpp : 361] Number of reads: 1414, Number of mercy edges: 25872
[cx1_seq2sdbg.cpp : 390] Done. Time elapsed: 0.2468
[cx1.h : 320] Preparing data... Done. Time elapsed: 0.2638
[cx1.h : 327] Preparing partitions and initialing global data...
[cx1_seq2sdbg.cpp : 516] 3 words per substring, num sequences: 299726, words per dummy node ($v): 2
[cx1_seq2sdbg.cpp : 549] Memory for sequence: 2547704
[cx1_seq2sdbg.cpp : 550] max # lv.1 items = 2097152
[cx1_seq2sdbg.cpp : 551] max # lv.2 items = 2097152
[cx1.h : 339] Preparing partitions and initialing global data... Done. Time elapsed: 0.0355
[cx1.h : 345] Start main loop...
[cx1.h : 366] Lv1 scanning from bucket 0 to 390625
[cx1.h : 378] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1099
[cx1.h : 437] Lv1 fetching & sorting done. Time elapsed: 0.1334
[cx1.h : 450] Main loop done. Time elapsed: 0.3226
[cx1.h : 456] Postprocessing...
[cx1_seq2sdbg.cpp : 962] Number of $ A C G T A- C- G- T-:
[cx1_seq2sdbg.cpp : 965] 10125 158135 139137 136721 157921 4730 4171 4165 4596
[cx1_seq2sdbg.cpp : 977] Total number of edges: 619701
[cx1_seq2sdbg.cpp : 978] Total number of ONEs: 591914
[cx1_seq2sdbg.cpp : 979] Total number of v$ edges: 10125
[cx1_seq2sdbg.cpp : 980] Total number of $v edges: 10125
[cx1.h : 464] Postprocess done. Time elapsed: 0.0211
[utils.h : 114] Real: 0.6439 user: 1.4920 sys: 0.6360 maxrss: 408056
--- [Fri Jun 19 16:01:35 2015] Assembling contigs from SdBG for k = 25 ---
cmd: /home/yifang/download-software/megahit_v0.3.0-beta_Linux_CUDA6.5_sm30/megahit_asm_core assemble -s S03/tmp/k25 -o S03/tmp/k25 -t 12 --max_tip_len -1 --min_standalone 368 --prune_level 2 --merge_len 20 --merge_similar 0.98 --low_local_ratio 0.2 --min_depth 2
[assembler.cpp : 155] Loading succinct de Bruijn graph: S03/tmp/k25
Error occurs when assembling contigs for k = 25
[Exit code -4]

Could you please give me some advice on this problem?
Thanks a lot!
Yifang

[voutcn]

Hi Yifang,

The reason is that your CPU does not support mpopcnt. Please check out the source codes in github, and compile megahit by make disablempopcnt=1.

[voutcn]

Hi @yifangt, have you solved the problem? If yes I can close this issue.

[yifangt]

Yes, that solved the problem.
Thanks a lot!