chensunefu commented 6 years ago

I used wtdbg-1.28 to assemble a 7g plant genome with about 70X pacbio data under default parameters (-L 5000) and got a ~6.5 g result. But, now I am assembling this genome using the same data with wtdbg2.1. The software stoped at indexing k-mers. I have tried several times. I think maybe there are some bugs in this version. Please could you check it? PS. I can get a poor results with 2.1 version when only used reads longer then 15 Kb.

ruanjue commented 6 years ago

Thanks for feedback.

When you said " stoped at indexing k-mers", does it mean program core dump, or cannot go on in indexing but alive?

chensunefu commented 6 years ago

Thanks for your quick response.

I attached the problem.

陈肃林木遗传育种国家重点实验室（东北林业大学） On 10/11/2018 10:58，Jue Ruannotifications@github.com wrote：

Thanks for feedback.

When you said " stoped at indexing k-mers", does it mean program core dump, or cannot go on in indexing but alive?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

ruanjue commented 6 years ago

I guess github cannot process attached files. Please send it to my email ruanjue@gmail.com, or paste it here.

chensunefu commented 6 years ago

The wtdbg2 cannot go on, it still alive but seems to be a zombie.

ruanjue commented 6 years ago

rm -f wtdbg2
make wtdbg2 DEBUG=1

gdb /path/to/wtdbg2
gdb> run -t 40 -i your_seqs.fa -p 19 ....

When you find the program stop in indexing

gdb> bt
gdb> info threads

Please also contact me.

chensunefu commented 6 years ago

Thanks so much. I will contact you once I meet problem or I get a result.

chensunefu commented 6 years ago

The program stop at index step. But now gdb doesnt response to any operations...... What can I do now?

ruanjue commented 6 years ago

paste the latest 40 lines in screen

chensunefu commented 6 years ago

0 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=132551813 7, ncpu=40) at kbm.h:905

1 0x000000000042e113 in build_nodes_graph (maxbp=18446744073709551615 , ncpu=40, pws=0x0, rdclip=1,

prefix=0x7fffffffe056 "wtdbg-5k", dump_kbm=0x0) at wtdbg.c:1265

2 0x0000000000472e7e in main (argc=13, argv=0x7fffffffdcf8) at wtdbg. c:6953

(gdb) info threads 84 Thread 0x7fff2e1fc700 (LWP 17278) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96b90) at kbm.h:745 83 Thread 0x7fff2ebfd700 (LWP 17277) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96aa0) at kbm.h:744 82 Thread 0x7fff2f5fe700 (LWP 17276) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe969b0) at kbm.h:744 81 Thread 0x7fff34dfa700 (LWP 17275) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe968c0) at kbm.h:744 80 Thread 0x7fff357fb700 (LWP 17274) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe967d0) at kbm.h:744 79 Thread 0x7fff361fc700 (LWP 17273) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe966e0) at kbm.h:745 78 Thread 0x7fff36bfd700 (LWP 17272) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe965f0) at kbm.h:745 77 Thread 0x7fff375fe700 (LWP 17271) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96500) at kbm.h:744 76 Thread 0x7fff3cdfa700 (LWP 17270) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96410) at kbm.h:745 75 Thread 0x7fff3d7fb700 (LWP 17269) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96320) at kbm.h:744 74 Thread 0x7fff3e1fc700 (LWP 17268) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96230) at kbm.h:745 73 Thread 0x7fff3ebfd700 (LWP 17267) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96140) at kbm.h:744 72 Thread 0x7fff3f5fe700 (LWP 17266) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96050) at kbm.h:744 71 Thread 0x7fff44dfa700 (LWP 17265) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95f60) at kbm.h:744 70 Thread 0x7fff457fb700 (LWP 17264) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95e70) at kbm.h:744 69 Thread 0x7fff461fc700 (LWP 17263) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95d80) at kbm.h:744 68 Thread 0x7fff46bfd700 (LWP 17262) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95c90) at kbm.h:745 ---Type to continue, or q to quit---return 67 Thread 0x7fff475fe700 (LWP 17261) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95ba0) at kbm.h:744 66 Thread 0x7fff4cdfa700 (LWP 17260) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95ab0) at kbm.h:744 65 Thread 0x7fff4d7fb700 (LWP 17259) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe959c0) at kbm.h:745 64 Thread 0x7fff4e1fc700 (LWP 17258) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe958d0) at kbm.h:744 63 Thread 0x7fff4ebfd700 (LWP 17257) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe957e0) at kbm.h:744 62 Thread 0x7fff4f5fe700 (LWP 17256) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe956f0) at kbm.h:745 61 Thread 0x7fff54d0f700 (LWP 17255) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95600) at kbm.h:744 60 Thread 0x7fff55710700 (LWP 17254) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95510) at kbm.h:744 59 Thread 0x7fff56111700 (LWP 17253) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95420) at kbm.h:745 58 Thread 0x7fffbeb71700 (LWP 17252) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95330) at kbm.h:745 57 Thread 0x7fffbf572700 (LWP 17251) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95240) at kbm.h:744 56 Thread 0x7fffbff73700 (LWP 17250) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95150) at kbm.h:745 55 Thread 0x7fffc0974700 (LWP 17249) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95060) at kbm.h:744 54 Thread 0x7fffc1375700 (LWP 17248) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94f70) at kbm.h:745 53 Thread 0x7fffc1d76700 (LWP 17247) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94e80) at kbm.h:745 52 Thread 0x7fffc2777700 (LWP 17246) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94d90) at kbm.h:745 51 Thread 0x7fffc3178700 (LWP 17245) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94ca0) at kbm.h:745 ---Type to continue, or q to quit--- 50 Thread 0x7fffc3b79700 (LWP 17244) 0x0000000000413c81 in thread_midx_func (obj=0x2fe94bb0) at kbm.h:744 49 Thread 0x7fffc457a700 (LWP 17243) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe94ac0) at kbm.h:745 48 Thread 0x7fffc4f7b700 (LWP 17241) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe949d0) at kbm.h:745 47 Thread 0x7ffff4eed700 (LWP 17240) 0x0000000000413c81 in thread_midx_func (obj=0x2fe948e0) at kbm.h:744 46 Thread 0x7ffff58ee700 (LWP 17239) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe947f0) at kbm.h:745 45 Thread 0x7ffff62ef700 (LWP 17238) 0x0000000000413c81 in thread_midx_func (obj=0x2fe94700) at kbm.h:744 44 Thread 0x7ffe37fff700 (LWP 17237) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 43 Thread 0x7ffe3ffff700 (LWP 17236) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 42 Thread 0x7ffe47fff700 (LWP 17235) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 41 Thread 0x7ffe4ffff700 (LWP 17234) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 40 Thread 0x7ffe57fff700 (LWP 17233) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 39 Thread 0x7ffe5ffff700 (LWP 17232) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 38 Thread 0x7ffe67fff700 (LWP 17231) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 37 Thread 0x7ffe6ffff700 (LWP 17230) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 36 Thread 0x7ffe77fff700 (LWP 17229) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 35 Thread 0x7ffe7ffff700 (LWP 17228) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 34 Thread 0x7ffe87fff700 (LWP 17227) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 33 Thread 0x7ffe8ffff700 (LWP 17226) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 32 Thread 0x7ffe97fff700 (LWP 17225) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 31 Thread 0x7ffe9ffff700 (LWP 17224) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 ---Type to continue, or q to quit--- 30 Thread 0x7ffea7fff700 (LWP 17223) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 29 Thread 0x7ffeaffff700 (LWP 17222) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 28 Thread 0x7ffeb7fff700 (LWP 17221) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 27 Thread 0x7ffebffff700 (LWP 17220) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 26 Thread 0x7ffec7fff700 (LWP 17219) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 25 Thread 0x7ffecffff700 (LWP 17218) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 24 Thread 0x7ffed7fff700 (LWP 17217) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 23 Thread 0x7ffedffff700 (LWP 17216) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 22 Thread 0x7ffee7fff700 (LWP 17215) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 21 Thread 0x7ffeeffff700 (LWP 17214) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 20 Thread 0x7ffef7fff700 (LWP 17213) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 19 Thread 0x7ffefffff700 (LWP 17212) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 18 Thread 0x7fff07fff700 (LWP 17211) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 17 Thread 0x7fff0ffff700 (LWP 17210) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 16 Thread 0x7fff17fff700 (LWP 17209) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 15 Thread 0x7fff1ffff700 (LWP 17208) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 14 Thread 0x7fff27fff700 (LWP 17207) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 ---Type to continue, or q to quit--- 13 Thread 0x7fff2ffff700 (LWP 17206) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 12 Thread 0x7fff37fff700 (LWP 17205) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 11 Thread 0x7fff3ffff700 (LWP 17204) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 10 Thread 0x7fff47fff700 (LWP 17203) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 9 Thread 0x7fff4ffff700 (LWP 17202) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 8 Thread 0x7fff56b12700 (LWP 17201) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 7 Thread 0x7fff57513700 (LWP 17200) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 6 Thread 0x7fff57f14700 (LWP 17199) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 5 Thread 0x7fff58915700 (LWP 17198) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 4 Thread 0x7ffff75b4700 (LWP 17197) 0x00000039d2e0ef3d in nanosleep () from /lib64/libpthread.so.0 2 Thread 0x7ffff7ff7700 (LWP 3714) 0x00000039d2ae53e7 in munmap () from /lib64/libc.so.6

1 Thread 0x7ffff7ff9700 (LWP 3709) 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=1325518137, ncpu=40) at kbm.h:905

ruanjue commented 6 years ago

Please give more lines back to program starting

chensunefu commented 6 years ago

All lines: (gdb) run -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 Starting program: /public/home/chensu/libraries/software/biosoft/wtdbg2-master/wtdbg2 -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 [Thread debugging using libthread_db enabled] [New Thread 0x7ffff7ff7700 (LWP 3714)]

-- total memory 529248448.0 kB -- available 506098668.0 kB -- 40 cores -- Starting program: /public/home/chensu/libraries/software/biosoft/wtdbg2-master/wtdbg2 -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 -- pid 3709 -- date Thu Oct 11 11:22:16 2018

[Thu Oct 11 11:22:16 2018] loading reads [New Thread 0x7ffff75b4700 (LWP 3715)] 12480000 13740000 22700000[Thread 0x7ffff75b4700 (LWP 3715) exited] 22705930 reads [Thu Oct 11 13:16:47 2018] Done, 22705930 reads, 342231416684 bp, 1325518137 bins PROC_STAT(0) : real 6871.235 sec, user 6371.410 sec, sys 1836.620 sec, maxrss 100623564.0 kB, maxvsize 110737088.0 kB [Thu Oct 11 13:16:48 2018] generating nodes, 40 threads [New Thread 0x7ffff75b4700 (LWP 17197)] [New Thread 0x7fff58915700 (LWP 17198)] [New Thread 0x7fff57f14700 (LWP 17199)] [New Thread 0x7fff57513700 (LWP 17200)] [New Thread 0x7fff56b12700 (LWP 17201)] [New Thread 0x7fff4ffff700 (LWP 17202)] [New Thread 0x7fff47fff700 (LWP 17203)] [New Thread 0x7fff3ffff700 (LWP 17204)] [New Thread 0x7fff37fff700 (LWP 17205)] [New Thread 0x7fff2ffff700 (LWP 17206)] [New Thread 0x7fff27fff700 (LWP 17207)] [New Thread 0x7fff1ffff700 (LWP 17208)] [New Thread 0x7fff17fff700 (LWP 17209)] [New Thread 0x7fff0ffff700 (LWP 17210)] [New Thread 0x7fff07fff700 (LWP 17211)] [New Thread 0x7ffefffff700 (LWP 17212)] [New Thread 0x7ffef7fff700 (LWP 17213)] [New Thread 0x7ffeeffff700 (LWP 17214)] [New Thread 0x7ffee7fff700 (LWP 17215)] [New Thread 0x7ffedffff700 (LWP 17216)] [New Thread 0x7ffed7fff700 (LWP 17217)] [New Thread 0x7ffecffff700 (LWP 17218)] [New Thread 0x7ffec7fff700 (LWP 17219)] [New Thread 0x7ffebffff700 (LWP 17220)] [New Thread 0x7ffeb7fff700 (LWP 17221)] [New Thread 0x7ffeaffff700 (LWP 17222)] [New Thread 0x7ffea7fff700 (LWP 17223)] [New Thread 0x7ffe9ffff700 (LWP 17224)] [New Thread 0x7ffe97fff700 (LWP 17225)] [New Thread 0x7ffe8ffff700 (LWP 17226)] [New Thread 0x7ffe87fff700 (LWP 17227)] [New Thread 0x7ffe7ffff700 (LWP 17228)] [New Thread 0x7ffe77fff700 (LWP 17229)] [New Thread 0x7ffe6ffff700 (LWP 17230)] [New Thread 0x7ffe67fff700 (LWP 17231)] [New Thread 0x7ffe5ffff700 (LWP 17232)] [New Thread 0x7ffe57fff700 (LWP 17233)] [New Thread 0x7ffe4ffff700 (LWP 17234)] [New Thread 0x7ffe47fff700 (LWP 17235)] [New Thread 0x7ffe3ffff700 (LWP 17236)] [New Thread 0x7ffe37fff700 (LWP 17237)] [Thu Oct 11 13:16:48 2018] indexing bins[0,1325518137] (339332643072 bp), 40 threads [New Thread 0x7ffff62ef700 (LWP 17238)] [New Thread 0x7ffff58ee700 (LWP 17239)] [New Thread 0x7ffff4eed700 (LWP 17240)] [New Thread 0x7fffc4f7b700 (LWP 17241)] [New Thread 0x7fffc457a700 (LWP 17243)] [New Thread 0x7fffc3b79700 (LWP 17244)] [New Thread 0x7fffc3178700 (LWP 17245)] [New Thread 0x7fffc2777700 (LWP 17246)] [New Thread 0x7fffc1d76700 (LWP 17247)] [New Thread 0x7fffc1375700 (LWP 17248)] [New Thread 0x7fffc0974700 (LWP 17249)] [New Thread 0x7fffbff73700 (LWP 17250)] [New Thread 0x7fffbf572700 (LWP 17251)] [New Thread 0x7fffbeb71700 (LWP 17252)] [New Thread 0x7fff56111700 (LWP 17253)] [New Thread 0x7fff55710700 (LWP 17254)] [New Thread 0x7fff54d0f700 (LWP 17255)] [New Thread 0x7fff4f5fe700 (LWP 17256)] [New Thread 0x7fff4ebfd700 (LWP 17257)] [New Thread 0x7fff4e1fc700 (LWP 17258)] [New Thread 0x7fff4d7fb700 (LWP 17259)] [New Thread 0x7fff4cdfa700 (LWP 17260)] [New Thread 0x7fff475fe700 (LWP 17261)] [New Thread 0x7fff46bfd700 (LWP 17262)] [New Thread 0x7fff461fc700 (LWP 17263)] [New Thread 0x7fff457fb700 (LWP 17264)] [New Thread 0x7fff44dfa700 (LWP 17265)] [New Thread 0x7fff3f5fe700 (LWP 17266)] [New Thread 0x7fff3ebfd700 (LWP 17267)] [New Thread 0x7fff3e1fc700 (LWP 17268)] [New Thread 0x7fff3d7fb700 (LWP 17269)] [New Thread 0x7fff3cdfa700 (LWP 17270)] [New Thread 0x7fff375fe700 (LWP 17271)] [New Thread 0x7fff36bfd700 (LWP 17272)] [New Thread 0x7fff361fc700 (LWP 17273)] [New Thread 0x7fff357fb700 (LWP 17274)] [New Thread 0x7fff34dfa700 (LWP 17275)] [New Thread 0x7fff2f5fe700 (LWP 17276)] [New Thread 0x7fff2ebfd700 (LWP 17277)] [New Thread 0x7fff2e1fc700 (LWP 17278)] [Thu Oct 11 13:16:49 2018] - scanning kmers (K0P19 subsampling 1/4) from 1325518137 bins 1325518137 bins PROC_STAT(0) : real 8158.797 sec, user 52729.840 sec, sys 2299.210 sec, maxrss 105694120.0 kB, maxvsize 121309508.0 kB [Thu Oct 11 13:38:15 2018] - Total kmers = 193701542 [Thu Oct 11 13:38:15 2018] - average kmer depth = 276 [Thu Oct 11 13:38:15 2018] - 1544 low frequency kmers (<2) [Thu Oct 11 13:38:15 2018] - 8949590 high frequency kmers (>1000) [Thu Oct 11 13:38:15 2018] - indexing 184751952 kmers, 33250593275 inst 0bt ^C

^C infor threads infr threads info threads ^C ^C ^C

Program received signal SIGINT, Interrupt. 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=1325518137, n 905 thread_apply_all(midx, midx->task = 6); Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el (gdb) (gdb) bt

0 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=132551813 7, ncpu=40) at kbm.h:905

1 0x000000000042e113 in build_nodes_graph (maxbp=18446744073709551615 , ncpu=40, pws=0x0, rdclip=1,

prefix=0x7fffffffe056 "wtdbg-5k", dump_kbm=0x0) at wtdbg.c:1265

2 0x0000000000472e7e in main (argc=13, argv=0x7fffffffdcf8) at wtdbg. c:6953

(gdb) info threads 84 Thread 0x7fff2e1fc700 (LWP 17278) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96b90) at kbm.h:745 83 Thread 0x7fff2ebfd700 (LWP 17277) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96aa0) at kbm.h:744 82 Thread 0x7fff2f5fe700 (LWP 17276) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe969b0) at kbm.h:744 81 Thread 0x7fff34dfa700 (LWP 17275) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe968c0) at kbm.h:744 80 Thread 0x7fff357fb700 (LWP 17274) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe967d0) at kbm.h:744 79 Thread 0x7fff361fc700 (LWP 17273) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe966e0) at kbm.h:745 78 Thread 0x7fff36bfd700 (LWP 17272) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe965f0) at kbm.h:745 77 Thread 0x7fff375fe700 (LWP 17271) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96500) at kbm.h:744 76 Thread 0x7fff3cdfa700 (LWP 17270) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96410) at kbm.h:745 75 Thread 0x7fff3d7fb700 (LWP 17269) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96320) at kbm.h:744 74 Thread 0x7fff3e1fc700 (LWP 17268) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe96230) at kbm.h:745 73 Thread 0x7fff3ebfd700 (LWP 17267) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96140) at kbm.h:744 72 Thread 0x7fff3f5fe700 (LWP 17266) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe96050) at kbm.h:744 71 Thread 0x7fff44dfa700 (LWP 17265) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95f60) at kbm.h:744 70 Thread 0x7fff457fb700 (LWP 17264) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95e70) at kbm.h:744 69 Thread 0x7fff461fc700 (LWP 17263) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95d80) at kbm.h:744 68 Thread 0x7fff46bfd700 (LWP 17262) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95c90) at kbm.h:745 ---Type to continue, or q to quit---return 67 Thread 0x7fff475fe700 (LWP 17261) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95ba0) at kbm.h:744 66 Thread 0x7fff4cdfa700 (LWP 17260) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95ab0) at kbm.h:744 65 Thread 0x7fff4d7fb700 (LWP 17259) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe959c0) at kbm.h:745 64 Thread 0x7fff4e1fc700 (LWP 17258) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe958d0) at kbm.h:744 63 Thread 0x7fff4ebfd700 (LWP 17257) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe957e0) at kbm.h:744 62 Thread 0x7fff4f5fe700 (LWP 17256) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe956f0) at kbm.h:745 61 Thread 0x7fff54d0f700 (LWP 17255) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95600) at kbm.h:744 60 Thread 0x7fff55710700 (LWP 17254) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95510) at kbm.h:744 59 Thread 0x7fff56111700 (LWP 17253) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95420) at kbm.h:745 58 Thread 0x7fffbeb71700 (LWP 17252) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95330) at kbm.h:745 57 Thread 0x7fffbf572700 (LWP 17251) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95240) at kbm.h:744 56 Thread 0x7fffbff73700 (LWP 17250) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe95150) at kbm.h:745 55 Thread 0x7fffc0974700 (LWP 17249) 0x0000000000413c81 in thread_mi dx_func (obj=0x2fe95060) at kbm.h:744 54 Thread 0x7fffc1375700 (LWP 17248) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94f70) at kbm.h:745 53 Thread 0x7fffc1d76700 (LWP 17247) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94e80) at kbm.h:745 52 Thread 0x7fffc2777700 (LWP 17246) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94d90) at kbm.h:745 51 Thread 0x7fffc3178700 (LWP 17245) 0x0000000000413ce1 in thread_mi dx_func (obj=0x2fe94ca0) at kbm.h:745 ---Type to continue, or q to quit--- 50 Thread 0x7fffc3b79700 (LWP 17244) 0x0000000000413c81 in thread_midx_func (obj=0x2fe94bb0) at kbm.h:744 49 Thread 0x7fffc457a700 (LWP 17243) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe94ac0) at kbm.h:745 48 Thread 0x7fffc4f7b700 (LWP 17241) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe949d0) at kbm.h:745 47 Thread 0x7ffff4eed700 (LWP 17240) 0x0000000000413c81 in thread_midx_func (obj=0x2fe948e0) at kbm.h:744 46 Thread 0x7ffff58ee700 (LWP 17239) 0x0000000000413ce1 in thread_midx_func (obj=0x2fe947f0) at kbm.h:745 45 Thread 0x7ffff62ef700 (LWP 17238) 0x0000000000413c81 in thread_midx_func (obj=0x2fe94700) at kbm.h:744 44 Thread 0x7ffe37fff700 (LWP 17237) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 43 Thread 0x7ffe3ffff700 (LWP 17236) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 42 Thread 0x7ffe47fff700 (LWP 17235) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 41 Thread 0x7ffe4ffff700 (LWP 17234) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 40 Thread 0x7ffe57fff700 (LWP 17233) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 39 Thread 0x7ffe5ffff700 (LWP 17232) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 38 Thread 0x7ffe67fff700 (LWP 17231) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 37 Thread 0x7ffe6ffff700 (LWP 17230) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 36 Thread 0x7ffe77fff700 (LWP 17229) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 35 Thread 0x7ffe7ffff700 (LWP 17228) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 34 Thread 0x7ffe87fff700 (LWP 17227) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 33 Thread 0x7ffe8ffff700 (LWP 17226) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 32 Thread 0x7ffe97fff700 (LWP 17225) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 31 Thread 0x7ffe9ffff700 (LWP 17224) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 ---Type to continue, or q to quit--- 30 Thread 0x7ffea7fff700 (LWP 17223) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 29 Thread 0x7ffeaffff700 (LWP 17222) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 28 Thread 0x7ffeb7fff700 (LWP 17221) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 27 Thread 0x7ffebffff700 (LWP 17220) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 26 Thread 0x7ffec7fff700 (LWP 17219) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 25 Thread 0x7ffecffff700 (LWP 17218) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 24 Thread 0x7ffed7fff700 (LWP 17217) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 23 Thread 0x7ffedffff700 (LWP 17216) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 22 Thread 0x7ffee7fff700 (LWP 17215) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 21 Thread 0x7ffeeffff700 (LWP 17214) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 20 Thread 0x7ffef7fff700 (LWP 17213) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 19 Thread 0x7ffefffff700 (LWP 17212) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 18 Thread 0x7fff07fff700 (LWP 17211) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 17 Thread 0x7fff0ffff700 (LWP 17210) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 16 Thread 0x7fff17fff700 (LWP 17209) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 15 Thread 0x7fff1ffff700 (LWP 17208) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 14 Thread 0x7fff27fff700 (LWP 17207) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 ---Type to continue, or q to quit--- 13 Thread 0x7fff2ffff700 (LWP 17206) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 12 Thread 0x7fff37fff700 (LWP 17205) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 11 Thread 0x7fff3ffff700 (LWP 17204) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 10 Thread 0x7fff47fff700 (LWP 17203) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 9 Thread 0x7fff4ffff700 (LWP 17202) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 8 Thread 0x7fff56b12700 (LWP 17201) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 7 Thread 0x7fff57513700 (LWP 17200) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 6 Thread 0x7fff57f14700 (LWP 17199) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 5 Thread 0x7fff58915700 (LWP 17198) 0x00000039d2e0b98e in pthread_cond_timedwait@@GLIBC_2.3.2 () ---Type to continue, or q to quit--- from /lib64/libpthread.so.0 4 Thread 0x7ffff75b4700 (LWP 17197) 0x00000039d2e0ef3d in nanosleep () from /lib64/libpthread.so.0 2 Thread 0x7ffff7ff7700 (LWP 3714) 0x00000039d2ae53e7 in munmap () from /lib64/libc.so.6

1 Thread 0x7ffff7ff9700 (LWP 3709) 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=1325518137, ncpu=40) at kbm.h:905 (gdb) c Continuing.

ruanjue commented 6 years ago

Thanks, I will contact you in email to debug the program.

chensunefu commented 6 years ago

Thanks for helping me to assemble this big genome.

ruanjue / wtdbg2

A 7g genome #22

0 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=132551813 7, ncpu=40) at kbm.h:905

1 0x000000000042e113 in build_nodes_graph (maxbp=18446744073709551615 , ncpu=40, pws=0x0, rdclip=1,

2 0x0000000000472e7e in main (argc=13, argv=0x7fffffffdcf8) at wtdbg. c:6953

All lines: (gdb) run -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 Starting program: /public/home/chensu/libraries/software/biosoft/wtdbg2-master/wtdbg2 -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 [Thread debugging using libthread_db enabled] [New Thread 0x7ffff7ff7700 (LWP 3714)]

-- total memory 529248448.0 kB -- available 506098668.0 kB -- 40 cores -- Starting program: /public/home/chensu/libraries/software/biosoft/wtdbg2-master/wtdbg2 -t 40 -i all.fa -p 19 -m 100 -fo wtdbg-5k -L 5000 -- pid 3709 -- date Thu Oct 11 11:22:16 2018

0 0x0000000000416072 in index_kbm (kbm=0x69e720, beg=0, end=132551813 7, ncpu=40) at kbm.h:905

1 0x000000000042e113 in build_nodes_graph (maxbp=18446744073709551615 , ncpu=40, pws=0x0, rdclip=1,

2 0x0000000000472e7e in main (argc=13, argv=0x7fffffffdcf8) at wtdbg. c:6953