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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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megahit v1.2.9 Exit code 11 #310

Open lcamVz opened 3 years ago

lcamVz commented 3 years ago

Good afternoon,

I left megahit running yesterday evening and came in today and came across theError code -11. Before successfully running megahit I had problems with fq.gz files but but after uncompressing them it ran fine until the error. I am running megahit through the conda environment. here is a copy of the log. I am running with dual intel xeon (10core 20 threads each) and 128gb RAM log.txt

jmwhitha commented 3 years ago

Good evening,

I'd really appreciate your help. I am also getting this same error running on a machine with 1Tb RAM (specified 900GB in the command). I don't think that its a memory issue. Here's my log with catchsegv executed.

(base) [jmwhitha@bridges2-login012 jmwhitha]$ cat slurm-3475261.out Continue mode activated. Ignore all options except for -o/--out-dir. 2021-09-03 16:08:37 - MEGAHIT v1.2.9 2021-09-03 16:08:37 - Using megahit_core without POPCNT and BMI2 support, because --no-hw-accel option manually specified 2021-09-03 16:08:37 - passing check point 0 2021-09-03 16:08:37 - passing check point 1 2021-09-03 16:08:37 - k-max reset to: 127 2021-09-03 16:08:37 - Start assembly. Number of CPU threads 24 2021-09-03 16:08:37 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-09-03 16:08:37 - Memory used: 900 2021-09-03 16:08:37 - passing check point 2 2021-09-03 16:08:37 - passing check point 3 2021-09-03 16:08:37 - passing check point 4 2021-09-03 16:08:37 - passing check point 5 2021-09-03 16:08:37 - passing check point 6 2021-09-03 16:08:37 - passing check point 7 2021-09-03 16:08:37 - passing check point 8 2021-09-03 16:08:37 - passing check point 9 2021-09-03 16:08:37 - passing check point 10 2021-09-03 16:08:37 - passing check point 11 2021-09-03 16:08:37 - passing check point 12 2021-09-03 16:08:37 - passing check point 13 2021-09-03 16:08:37 - passing check point 14 2021-09-03 16:08:37 - passing check point 15 2021-09-03 16:08:37 - passing check point 16 2021-09-03 16:08:37 - passing check point 17 2021-09-03 16:08:37 - passing check point 18 2021-09-03 16:08:37 - Assemble contigs from SdBG for k = 67 2021-09-03 16:27:28 - Error occurs, please refer to /ocean/projects/agr200001p/jmwhitha/MEGAHITout19/log for detail 2021-09-03 16:27:28 - Command: /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt assemble -s /ocean/projects/agr200001p/jmwhitha/MEGAHITout19/tmp/k67/67 -o /ocean/projects/agr200001p/jmwhitha/MEGAHITout19/intermediate_contigs/k67 -t 24 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble; Exit code -11 *** Segmentation fault Register dump:

RAX: ffffffffffffffff RBX: 00007ffc1abc1e40 RCX: 0000000000000010 RDX: 0000000000000004 RSI: 000000000f0e6af8 RDI: 00007ffc1abc1e40 RBP: 0000000000000021 R8 : 00000011854f64b3 R9 : 00000000003c39ab R10: 000014a31e776010 R11: 03ffffffffffffff R12: 0000000f0e6af7e1 R13: 000014a035363010 R14: 0000000000000000 R15: 000014a035363010 RSP: 0000149e0c937de0

RIP: 0000558cbf9e5185 EFLAGS: 00010a07

CS: 0033 FS: 0000 GS: 0000

Trap: 0000000d Error: 00000000 OldMask: 00000000 CR2: 00000000

FPUCW: 0000037f FPUSW: 00000000 TAG: 00000000 RIP: 00000000 RDP: 00000000

ST(0) 0000 0000000000000000 ST(1) 0000 0000000000000000 ST(2) 0000 0000000000000000 ST(3) 0000 0000000000000000 ST(4) 0000 0000000000000000 ST(5) 0000 0000000000000000 ST(6) 0000 0000000000000000 ST(7) 0000 0000000000000000 mxcsr: 1fa0 XMM0: 00000000000000000000000000000000 XMM1: 00000000000000000000000000000000 XMM2: 00000000000000000000000000000000 XMM3: 00000000000000000000000000000000 XMM4: 00000000000000000000000000000000 XMM5: 00000000000000000000000000000000 XMM6: 00000000000000000000000000000000 XMM7: 00000000000000000000000000000000 XMM8: 00000000000000000000000000000000 XMM9: 00000000000000000000000000000000 XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000 XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000 XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000

Backtrace: /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt(+0xdc082)[0x558cbf9e5082] /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/../lib/libgomp.so.1(+0x1465f)[0x14c34cbf665f] /lib64/libpthread.so.0(+0x82de)[0x14c34c3fe2de] /lib64/libc.so.6(clone+0x43)[0x14c34c12fe83]

Memory map:

149e08000000-149e08021000 rw-p 00000000 00:00 0 149e08021000-149e0c000000 ---p 00000000 00:00 0 149e0c336000-149e0c337000 ---p 00000000 00:00 0 149e0c337000-149e0c537000 rw-p 00000000 00:00 0 149e0c537000-149e0c538000 ---p 00000000 00:00 0 149e0c538000-149e0c738000 rw-p 00000000 00:00 0 149e0c738000-149e0c739000 ---p 00000000 00:00 0 149e0c739000-149e0c939000 rw-p 00000000 00:00 0 149e0c939000-149e0c93a000 ---p 00000000 00:00 0 149e0c93a000-149e0cb3a000 rw-p 00000000 00:00 0 149e0cb3a000-149e0cb3b000 ---p 00000000 00:00 0 149e0cb3b000-149e0cd3b000 rw-p 00000000 00:00 0 149e0cd3b000-149e0cd3c000 ---p 00000000 00:00 0 149e0cd3c000-149e0cf3c000 rw-p 00000000 00:00 0 149e0cf3c000-149e0cf3d000 ---p 00000000 00:00 0 149e0cf3d000-149e0d13d000 rw-p 00000000 00:00 0 149e0d13d000-149e0d13e000 ---p 00000000 00:00 0 149e0d13e000-149e0d33e000 rw-p 00000000 00:00 0 149e0d33e000-149e0d33f000 ---p 00000000 00:00 0 149e0d33f000-149e0d53f000 rw-p 00000000 00:00 0 149e0d53f000-149e0d540000 ---p 00000000 00:00 0 149e0d540000-149e0d740000 rw-p 00000000 00:00 0 149e0d740000-149e0d741000 ---p 00000000 00:00 0 149e0d741000-149e0d941000 rw-p 00000000 00:00 0 149e0d941000-149e0d942000 ---p 00000000 00:00 0 149e0d942000-149e0db42000 rw-p 00000000 00:00 0 149e0db42000-149e0db43000 ---p 00000000 00:00 0 149e0db43000-149e0dd43000 rw-p 00000000 00:00 0 149e0dd43000-149e0dd44000 ---p 00000000 00:00 0 149e0dd44000-149e0df44000 rw-p 00000000 00:00 0 149e0df44000-149e0df45000 ---p 00000000 00:00 0 149e0df45000-149e0e145000 rw-p 00000000 00:00 0 149e0e145000-149e0e146000 ---p 00000000 00:00 0 149e0e146000-149e0e346000 rw-p 00000000 00:00 0 149e0e346000-149e0e347000 ---p 00000000 00:00 0 149e0e347000-149e0e547000 rw-p 00000000 00:00 0 149e0e547000-149e0e548000 ---p 00000000 00:00 0 149e0e548000-149e0e748000 rw-p 00000000 00:00 0 149e0e748000-149e0e749000 ---p 00000000 00:00 0 149e0e749000-14c34b52f000 rw-p 00000000 00:00 0 14c34b62c000-14c34b62d000 ---p 00000000 00:00 0 14c34b62d000-14c34b82d000 rw-p 00000000 00:00 0 14c34b82d000-14c34b82e000 ---p 00000000 00:00 0 14c34b82e000-14c34ba2e000 rw-p 00000000 00:00 0 14c34ba2e000-14c34ba2f000 ---p 00000000 00:00 0 14c34ba2f000-14c34bc2f000 rw-p 00000000 00:00 0 14c34bc2f000-14c34bc30000 ---p 00000000 00:00 0 14c34bc30000-14c34be30000 rw-p 00000000 00:00 0 14c34be30000-14c34be33000 r-xp 00000000 103:03 10455142 /usr/lib64/libdl-2.28.so 14c34be33000-14c34c032000 ---p 00003000 103:03 10455142 /usr/lib64/libdl-2.28.so 14c34c032000-14c34c033000 r--p 00002000 103:03 10455142 /usr/lib64/libdl-2.28.so 14c34c033000-14c34c034000 rw-p 00003000 103:03 10455142 /usr/lib64/libdl-2.28.so 14c34c034000-14c34c1ed000 r-xp 00000000 103:03 10455138 /usr/lib64/libc-2.28.so 14c34c1ed000-14c34c3ec000 ---p 001b9000 103:03 10455138 /usr/lib64/libc-2.28.so 14c34c3ec000-14c34c3f0000 r--p 001b8000 103:03 10455138 /usr/lib64/libc-2.28.so 14c34c3f0000-14c34c3f2000 rw-p 001bc000 103:03 10455138 /usr/lib64/libc-2.28.so 14c34c3f2000-14c34c3f6000 rw-p 00000000 00:00 0 14c34c3f6000-14c34c411000 r-xp 00000000 103:03 10455079 /usr/lib64/libpthread-2.28.so 14c34c411000-14c34c610000 ---p 0001b000 103:03 10455079 /usr/lib64/libpthread-2.28.so 14c34c610000-14c34c611000 r--p 0001a000 103:03 10455079 /usr/lib64/libpthread-2.28.so 14c34c611000-14c34c612000 rw-p 0001b000 103:03 10455079 /usr/lib64/libpthread-2.28.so 14c34c612000-14c34c616000 rw-p 00000000 00:00 0 14c34c616000-14c34c797000 r-xp 00000000 103:03 10455146 /usr/lib64/libm-2.28.so 14c34c797000-14c34c996000 ---p 00181000 103:03 10455146 /usr/lib64/libm-2.28.so 14c34c996000-14c34c997000 r--p 00180000 103:03 10455146 /usr/lib64/libm-2.28.so 14c34c997000-14c34c998000 rw-p 00181000 103:03 10455146 /usr/lib64/libm-2.28.so 14c34c998000-14c34c99c000 r-xp 00000000 103:03 10455132 /usr/lib64/libSegFault.so 14c34c99c000-14c34cb9b000 ---p 00004000 103:03 10455132 /usr/lib64/libSegFault.so 14c34cb9b000-14c34cb9c000 r--p 00003000 103:03 10455132 /usr/lib64/libSegFault.so 14c34cb9c000-14c34cb9d000 rw-p 00004000 103:03 10455132 /usr/lib64/libSegFault.so 14c34cb9d000-14c34cbc6000 r-xp 00000000 103:03 10455124 /usr/lib64/ld-2.28.so 14c34cbc7000-14c34cbce000 rw-p 00000000 00:00 0 14c34cbce000-14c34cbd1000 r--p 00000000 9eb:8126a 144120807570865270 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgcc_s.so.1 14c34cbd1000-14c34cbdd000 r-xp 00003000 9eb:8126a 144120807570865270 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgcc_s.so.1 14c34cbdd000-14c34cbe0000 r--p 0000f000 9eb:8126a 144120807570865270 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgcc_s.so.1 14c34cbe0000-14c34cbe1000 r--p 00011000 9eb:8126a 144120807570865270 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgcc_s.so.1 14c34cbe1000-14c34cbe2000 rw-p 00012000 9eb:8126a 144120807570865270 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgcc_s.so.1 14c34cbe2000-14c34cbec000 r--p 00000000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cbec000-14c34cc03000 r-xp 0000a000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cc03000-14c34cc0c000 r--p 00021000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cc0c000-14c34cc0d000 ---p 0002a000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cc0d000-14c34cc0e000 r--p 0002a000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cc0e000-14c34cc0f000 rw-p 0002b000 9eb:8126a 144120807570865056 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libgomp.so.1.0.0 14c34cc2e000-14c34ccd1000 r--p 00000000 9eb:8126a 144120807570872191 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libstdc++.so.6.0.28 14c34ccd1000-14c34cd50000 r-xp 000a3000 9eb:8126a 144120807570872191 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libstdc++.so.6.0.28 14c34cd50000-14c34cd91000 r--p 00122000 9eb:8126a 144120807570872191 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libstdc++.so.6.0.28 14c34cd91000-14c34cd9c000 r--p 00162000 9eb:8126a 144120807570872191 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libstdc++.so.6.0.28 14c34cd9c000-14c34cda0000 rw-p 0016d000 9eb:8126a 144120807570872191 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libstdc++.so.6.0.28 14c34cda0000-14c34cda3000 rw-p 00000000 00:00 0 14c34cda3000-14c34cda6000 r--p 00000000 9eb:8126a 144120807570871484 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libz.so.1.2.11 14c34cda6000-14c34cdba000 r-xp 00003000 9eb:8126a 144120807570871484 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libz.so.1.2.11 14c34cdba000-14c34cdc1000 r--p 00017000 9eb:8126a 144120807570871484 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libz.so.1.2.11 14c34cdc1000-14c34cdc2000 r--p 0001d000 9eb:8126a 144120807570871484 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libz.so.1.2.11 14c34cdc2000-14c34cdc3000 rw-p 0001e000 9eb:8126a 144120807570871484 /ocean/projects/agr200001p/jmwhitha/assembly_env/lib/libz.so.1.2.11 14c34cdc3000-14c34cdc5000 rw-p 00000000 00:00 0 14c34cdc5000-14c34cdc6000 r--p 00028000 103:03 10455124 /usr/lib64/ld-2.28.so 14c34cdc6000-14c34cdc7000 rw-p 00029000 103:03 10455124 /usr/lib64/ld-2.28.so 14c34cdc7000-14c34cdc8000 rw-p 00000000 00:00 0 558cbf909000-558cbf92d000 r--p 00000000 9eb:8126a 144120807570865081 /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt 558cbf92d000-558cbfb5d000 r-xp 00024000 9eb:8126a 144120807570865081 /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt 558cbfb5d000-558cbfb9c000 r--p 00254000 9eb:8126a 144120807570865081 /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt 558cbfb9c000-558cbfb9e000 r--p 00292000 9eb:8126a 144120807570865081 /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt 558cbfb9e000-558cbfb9f000 rw-p 00294000 9eb:8126a 144120807570865081 /ocean/projects/agr200001p/jmwhitha/assembly_env/bin/megahit_core_popcnt 558cbfb9f000-558cbfba1000 rw-p 00000000 00:00 0 558cc0f26000-558cc219a000 rw-p 00000000 00:00 0 [heap] 7ffc1aba3000-7ffc1abc5000 rw-p 00000000 00:00 0 [stack] 7ffc1abe7000-7ffc1abea000 r--p 00000000 00:00 0 [vvar] 7ffc1abea000-7ffc1abec000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

USMortality commented 2 months ago

I'm seeing this error sporadically happen, even with the test command:

FROM alpine:latest

RUN apk update && apk add --no-cache python3 && \
  wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz && \
  mkdir /megahit && tar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz --strip-components=1 -C /megahit && \ 
  rm MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
ENV PATH="/megahit/bin:${PATH}"
WORKDIR /data

ENTRYPOINT ["megahit"]
docker build . -t megahit -f ./Dockerfile
docker run megahit --test
2024-07-06 10:37:05 - Build graph for k = 21 
2024-07-06 10:37:05 - Error occurs, please refer to /tmp/megahit_test_r80i83ja/log for detail
2024-07-06 10:37:05 - Command: /megahit/bin/megahit_core_popcnt seq2sdbg --host_mem 15077630361 --mem_flag 1 --output_prefix /tmp/megahit_test_r80i83ja/tmp/k21/21 --num_cpu_threads 8 -k 21 --kmer_from 0 --input_prefix /tmp/megahit_test_r80i83ja/tmp/k21/21 --need_mercy; Exit code -11

For me, this typically works 3/4 times or so... but randomly fails...