Assertion failed

[sjaenick]

1.2.8 release, two attempts failed here:

2019-09-14 10:09:04 - Assemble contigs from SdBG for k = 21
2019-09-14 10:09:04 - command /ceph/mgx-sw/bin/megahit_core_popcnt assemble -s /ceph/sge-tmp/MGX2_devel/10/a20ee79fd94912d2a52b
bf3a42359c45/megahit_out/tmp/k21/21 -o /ceph/sge-tmp/MGX2_devel/10/a20ee79fd94912d2a52bbf3a42359c45/megahit_out/intermediate_co
ntigs/k21 -t 39 --min_standalone 1000 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_rati
o 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble
2019-09-14 12:02:37 - INFO  main_assemble.cpp             :  129 - Loading succinct de Bruijn graph: /ceph/sge-tmp/MGX2_devel/1
0/a20ee79fd94912d2a52bbf3a42359c45/megahit_out/tmp/k21/21Done. Time elapsed: 6813.346662
2019-09-14 12:02:37 - INFO  main_assemble.cpp             :  133 - Number of Edges: 37847905941; K value: 21
2019-09-14 12:02:37 - INFO  main_assemble.cpp             :  140 - Number of CPU threads: 39
2019-09-14 12:38:01 - INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 2; Accumulated tips remo
ved: 159584137; time elapsed: 228.9040
2019-09-14 12:43:16 - INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 4; Accumulated tips removed: 270250007; time elapsed: 315.3061
2019-09-14 12:50:58 - INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 8; Accumulated tips removed: 353051795; time elapsed: 461.3341
2019-09-14 13:03:23 - INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 16; Accumulated tips removed: 427543988; time elapsed: 745.0272
2019-09-14 13:20:37 - INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 32; Accumulated tips removed: 486940419; time elapsed: 1034.6756
2019-09-14 13:36:32 - INFO  assembly/sdbg_pruning.cpp     :  169 - Removing tips with length less than 42; Accumulated tips removed: 505295443; time elapsed: 954.8256
2019-09-14 13:36:33 - INFO  main_assemble.cpp             :  158 - Tips removal done! Time elapsed(sec): 5635.792
2019-09-14 23:40:19 - INFO  assembly/unitig_graph.cpp     :   84 - Graph size without loops: 2485161669, palindrome: 214170
2019-09-15 03:10:58 - INFO  main_assemble.cpp             :  167 - unitig graph size: 2485238965, time for building: 48865.691
2019-09-15 16:57:06 - INFO  assembly/contig_stat.h        :   40 - Max: 3092, Min: 22, N50: 24, number contigs: 2485238965, number isolated: 4734484, number looped: 77296, total size: 68834473749,
2019-09-15 16:57:06 - [ERROR] Cannot stat: No such file or directory
2019-09-15 16:57:06 - INFO  main_assemble.cpp             :  184 - Graph cleaning round 1
2019-09-15 17:35:29 - INFO  main_assemble.cpp             :  201 - Number of bubbles removed: 4951563, Time elapsed(sec): 2303.203
2019-09-15 18:13:36 - INFO  main_assemble.cpp             :  211 - Number of complex bubbles removed: 1059122, Time elapsed(sec): 2287.004338
2019-09-15 19:15:46 - megahit_core_popcnt: /homes/sjaenick/megahit/src/assembly/unitig_graph.cpp:315: void UnitigGraph::Refresh(bool): Assertion `!(next_adapter.GetFlag() & kDeleted)' failed.
2019-09-15 21:22:56 - Error occurs, please refer to /ceph/sge-tmp/MGX2_devel/10/a20ee79fd94912d2a52bbf3a42359c45/megahit_out/log for detail
2019-09-15 21:22:56 - Command: /ceph/mgx-sw/bin/megahit_core_popcnt assemble -s /ceph/sge-tmp/MGX2_devel/10/a20ee79fd94912d2a52bbf3a42359c45/megahit_out/tmp/k21/21 -o /ceph/sge-tmp/MGX2_devel/10/a20ee79fd94912d2a52bbf3a42359c45/megahit_out/intermediate_contigs/k21 -t 39 --min_standalone 1000 --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 -6

[voutcn]

Short answer:
Please just compile with -DCMAKE_BUILD_TYPE=Release to ignore the assertion.

The assertion is incorrect. It is okay to remove it. I am yet to come out with a toy example and add it as a test case.

The released binary was compiled with -DCMAKE_BUILD_TYPE=Release which will ignore all assertions. So users who use pre-compiled binaries are not affected.

@spongebob22 encountered the same issue. While it failed on the server, the assembly was successful on a local machine. I guess the binaries on the local machine was compiled with the release flag while that on the server was not.

[sjaenick]

Thanks, I'll do that.

[hrazif]

Hello!

I am running to the same error, "exit code -6". I installed megahit using conda.

I found out that I can avoid this error when specifying just one CPU core (-t 1). But, the run takes a very long time using just one core. I would like to be able to run megahit with 10-20 cores, if possible.

I would appreciate your help.

[marlaux]

Hello, could someone please explain to me what it means "compile with"? I don't know what I should do:
"Please just compile with -DCMAKE_BUILD_TYPE=Release to ignore the assertion."
Thank you very much

[johannalheureux23]

@marlaux I have the same question as you...did you ever figure out what 'compile with -DCMAKE_BUILD_TYPE=Release' meant?