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I saw a similar issue but the responses did not help me solve the problem, so i thought i'd post as a new issue.
The program stops at assembling at contig k = 27. I tried with --kmin-1pass option but it didn't help. I thought maybe it was a memory issue so i capped that with “-m 0.5“, and that still did not fix the issue. I am running on a server where megahit comes complied and i just have to load the correct software as follows:
I contacted the bioinformaticians that maintain the server but they said it does "Its Most likely this is caused by a problem with the code and so, I think contacting the megahit authors could be your best bet."
I get a large core file that i can attached but its >3GB, and here is the output of the log file:
2019-09-17 10:25:47 – MEGAHIT v1.2.7
2019-09-17 10:25:47 – Using megahit_core with POPCNT and BMI2 support
2019-09-17 10:25:47 – Convert reads to binary library
2019-09-17 10:25:47 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core buildlib /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib
2019-09-17 10:27:48 – INFO sequence/io/sequence_lib.cpp : 77 – Lib 0 (/home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/trimreads/SEEP_BRIDGE_DI_R1_P_trimmed.fq.gz,/home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/trimreads/SEEP_BRIDGE_DI_R2_P_trimmed.fq.gz): pe, 72595302 reads, 151 max length
2019-09-17 10:27:48 – INFO utils/utils.h : 152 – Real: 120.5771 user: 91.9506 sys: 21.9402 maxrss: 247472
2019-09-17 10:27:48 – Start assembly. Number of CPU threads 16
2019-09-17 10:27:48 – k list: 27,37,47,57,67,77,87,97,107,117,127,137,147
2019-09-17 10:27:48 – Memory used: 67537805312
2019-09-17 10:27:48 – Extract solid (k+1)-mers for k = 27
2019-09-17 10:27:48 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core count -k 27 -m 2 –host_mem 67537805312.0 –mem_flag 1 –output_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –num_cpu_threads 16 –read_lib_file /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib
2019-09-17 10:27:48 – INFO sorting/base_engine.cpp : 148 – Preparing data…
2019-09-17 10:27:48 – INFO sequence/io/sequence_lib.cpp : 115 – Before reading, sizeof seq_package: 3215614856
2019-09-17 10:27:57 – INFO sequence/io/sequence_lib.cpp : 117 – After reading, sizeof seq_package: 3215614856
2019-09-17 10:27:57 – INFO sorting/kmer_counter.cpp : 76 – 72595302 reads, 151 max read length
2019-09-17 10:27:57 – INFO sorting/kmer_counter.cpp : 83 – 2 words per substring, 3 words per edge
2019-09-17 10:27:57 – INFO sorting/base_engine.cpp : 153 – Preparing data… Done. Time elapsed: 9.6948
2019-09-17 10:27:57 – INFO sorting/base_engine.cpp : 156 – Preparing partitions and calculating bucket sizes…
2019-09-17 10:28:08 – INFO sorting/base_engine.cpp : 80 – Minimum memory required: 4202744292 bytes
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 138 – Lv1 items: 1143937871, Lv2 items: 6283824
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 140 – Memory of derived class: 3887105048, Memory for Lv1+Lv2: 4676292668
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 168 – Preparing partitions and calculating bucket sizes… Done. Time elapsed: 13.4045
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 172 – Start main loop…
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 0 to 1046
2019-09-17 10:28:24 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 12.8581
2019-09-17 10:28:40 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 16.9110
2019-09-17 10:28:40 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 1046 to 3148
2019-09-17 10:28:54 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 13.6388
2019-09-17 10:29:14 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 19.5220
2019-09-17 10:29:14 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 3148 to 6238
2019-09-17 10:29:28 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.1731
2019-09-17 10:29:49 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 21.2304
2019-09-17 10:29:49 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 6238 to 10512
2019-09-17 10:30:04 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.7469
2019-09-17 10:30:26 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 22.0881
2019-09-17 10:30:26 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 10512 to 16434
2019-09-17 10:30:41 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 15.2846
2019-09-17 10:31:04 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 23.1813
2019-09-17 10:31:04 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 16434 to 24991
2019-09-17 10:31:20 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 15.6392
2019-09-17 10:31:44 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 24.0282
2019-09-17 10:31:44 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 24991 to 39394
2019-09-17 10:32:00 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 16.1445
2019-09-17 10:32:26 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 25.6580
2019-09-17 10:32:26 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 39394 to 65536
2019-09-17 10:32:40 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.1519
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 16.3075
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 204 – Main loop done. Time elapsed: 285.5726
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 207 – Postprocessing…
2019-09-17 10:33:00 – INFO sorting/kmer_counter.cpp : 406 – Total number of candidate reads: 4537891 (16253539)
2019-09-17 10:33:00 – INFO sorting/kmer_counter.cpp : 408 – Total number of solid edges: 948756888
2019-09-17 10:33:00 – INFO sorting/base_engine.cpp : 210 – Postprocess done. Time elapsed: 4.0569
2019-09-17 10:33:01 – INFO utils/utils.h : 152 – Real: 313.4382 user: 4613.5264 sys: 106.0754 maxrss: 8399168
2019-09-17 10:33:01 – Build graph for k = 27
2019-09-17 10:33:01 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core seq2sdbg –host_mem 67537805312.0 –mem_flag 1 –output_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –num_cpu_threads 16 -k 27 –kmer_from 0 –input_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –need_mercy
2019-09-17 10:33:01 – INFO sorting/base_engine.cpp : 148 – Preparing data…
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 369 – Number edges: 948756888
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 415 – Bases to reserve: 33206491080, number contigs: 0, number multiplicity: 1185946110
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 422 – Before reading, sizeof seq_package: 8301622780, multiplicity vector: 1185946110
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 428 – Read 948756888 edges.
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 433 – After reading, sizeof seq_package: 8301622780/948756888/26565192864, multiplicity vector: 948756888/1185946110
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 440 – Adding mercy edges…
2019-09-17 10:34:04 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:05 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:06 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:08 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:09 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:10 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:11 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:13 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:15 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:16 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:17 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:18 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:20 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:21 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:22 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:23 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:24 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:26 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:27 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:28 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:29 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:31 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:32 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:33 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:34 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:36 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:37 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:38 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:39 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:41 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:42 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:43 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:44 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:46 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:47 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:48 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:49 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:51 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:52 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:53 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:54 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:56 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:57 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:58 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:59 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:01 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:02 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:03 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:04 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:05 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:07 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:08 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:09 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:10 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:12 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:13 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:14 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:15 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:17 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:18 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:19 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:20 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:22 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:23 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:24 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:25 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:27 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:28 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:29 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:30 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 15907 reads to search for mercy k-mers
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 356 – Number of reads: 4537891, Number of mercy edges: 137033696
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 444 – Done. Time elapsed: 108.5788
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 449 – After adding mercy, sizeof seq_package: 8301622780/1085790584/30402136352, multiplicity vector: 1085790584/1185946110
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 508 – Finally, sizeof seq_package: 8301622780/1085790584/30402136352, multiplicity vector: 1085790584/1185946110
2019-09-17 10:35:31 – INFO sorting/base_engine.cpp : 153 – Preparing data… Done. Time elapsed: 149.6824
2019-09-17 10:35:31 – INFO sorting/base_engine.cpp : 156 – Preparing partitions and calculating bucket sizes…
2019-09-17 10:35:40 – INFO sorting/base_engine.cpp : 80 – Minimum memory required: 11139101008 bytes
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 138 – Lv1 items: 868632467, Lv2 items: 4771536
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 140 – Memory of derived class: 10911031720, Memory for Lv1+Lv2: 3531788300
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 168 – Preparing partitions and calculating bucket sizes… Done. Time elapsed: 11.6378
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 172 – Start main loop…
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 0 to 1575
2019-09-17 10:35:53 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 10.5633
2019-09-17 10:36:03 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.3918
2019-09-17 10:36:03 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 1575 to 4689
2019-09-17 10:36:10 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.6244
2019-09-17 10:36:21 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.8340
2019-09-17 10:36:21 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 4689 to 9223
2019-09-17 10:36:28 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.7369
2019-09-17 10:36:39 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.9330
2019-09-17 10:36:39 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 9223 to 15277
2019-09-17 10:36:46 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.9538
2019-09-17 10:36:57 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.9638
2019-09-17 10:36:57 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 15277 to 23201
2019-09-17 10:37:04 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.4609
2019-09-17 10:37:15 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.0484
2019-09-17 10:37:15 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 23201 to 33750
2019-09-17 10:37:23 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.4965
2019-09-17 10:37:34 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.1667
2019-09-17 10:37:34 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 33750 to 49499
2019-09-17 10:37:42 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.7935
2019-09-17 10:37:53 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.2160
2019-09-17 10:37:53 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 49499 to 65536
2019-09-17 10:37:59 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.2833
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 5.8518
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 204 – Main loop done. Time elapsed: 142.3261
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 207 – Postprocessing…
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 793 – Number of $ A C G T A- C- G- T-:
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 794 – 14742369 455415904 633657824 635116617 455152761 1084447 2405351 2421353 1067631
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 800 – Total number of edges: 2201064257
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 801 – Total number of ONEs: 2179343106
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 803 – Total number of $v edges: 14742369
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 210 – Postprocess done. Time elapsed: 0.0642
2019-09-17 10:38:06 – INFO utils/utils.h : 152 – Real: 304.9620 user: 3416.7373 sys: 71.1459 maxrss: 13081104
2019-09-17 10:38:06 – Assemble contigs from SdBG for k = 27
2019-09-17 10:38:06 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core assemble -s /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 -o /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/intermediate_contigs/k27 -t 16 –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
2019-09-17 10:38:53 – INFO main_assemble.cpp : 129 – Loading succinct de Bruijn graph: /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27Done. Time elapsed: 47.008568
2019-09-17 10:38:53 – INFO main_assemble.cpp : 133 – Number of Edges: 2201064257; K value: 27
2019-09-17 10:38:53 – INFO main_assemble.cpp : 140 – Number of CPU threads: 16
2019-09-17 10:39:20 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 2; Accumulated tips removed: 368650; time elapsed: 2.6854
2019-09-17 10:39:25 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 4; Accumulated tips removed: 1100561; time elapsed: 4.6705
2019-09-17 10:39:35 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 8; Accumulated tips removed: 2089344; time elapsed: 10.1763
2019-09-17 10:39:57 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 16; Accumulated tips removed: 3621395; time elapsed: 21.7634
2019-09-17 10:40:37 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 32; Accumulated tips removed: 5806553; time elapsed: 39.9274
2019-09-17 10:41:33 – INFO assembly/sdbg_pruning.cpp : 169 – Removing tips with length less than 54; Accumulated tips removed: 7829599; time elapsed: 56.6510
2019-09-17 10:41:33 – INFO main_assemble.cpp : 158 – Tips removal done! Time elapsed(sec): 160.040
2019-09-17 10:45:02 – INFO assembly/unitig_graph.cpp : 84 – Graph size without loops: 12073549, palindrome: 1500
2019-09-17 10:45:12 – INFO main_assemble.cpp : 167 – unitig graph size: 12085257, time for building: 218.576
2019-09-17 10:45:32 – INFO assembly/contig_stat.h : 40 – Max: 23761, Min: 28, N50: 147, number contigs: 12085257, number isolated: 3153332, number looped: 11708, total size: 1332397452,
2019-09-17 10:45:32 – INFO main_assemble.cpp : 184 – Graph cleaning round 1
2019-09-17 10:45:47 – INFO main_assemble.cpp : 201 – Number of bubbles removed: 727321, Time elapsed(sec): 14.906
2019-09-17 10:45:56 – INFO main_assemble.cpp : 211 – Number of complex bubbles removed: 219193, Time elapsed(sec): 9.180119
2019-09-17 10:45:59 – INFO main_assemble.cpp : 222 – Number unitigs disconnected: 591974, time: 2.664
2019-09-17 10:46:00 – INFO main_assemble.cpp : 246 – Unitigs removed in excessive pruning: 808, time: 1.403
2019-09-17 10:46:00 – INFO main_assemble.cpp : 184 – Graph cleaning round 2
2019-09-17 10:46:07 – INFO main_assemble.cpp : 192 – Tips removed: 127963, time: 6.796
2019-09-17 10:46:09 – megahit_core: /dev/shm/ebuser/avx2/MEGAHIT/1.2.7/gmklc-2018.3.100/megahit-1.2.7/src/assembly/unitig_graph.cpp:315: void UnitigGraph::Refresh(bool): Assertion `!(next_adapter.GetFlag() & kDeleted)’ failed.
2019-09-17 10:46:30 – Error occurs, please refer to /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/log for detail
2019-09-17 10:46:30 – Command: /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core assemble -s /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 -o /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/intermediate_contigs/k27 -t 16 –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 -6
In the mean time i have assembled this sample locally on my own workstation - so it something to do with it being on a server? Any thoughts much appreciated.
Thanks!
The text was updated successfully, but these errors were encountered:
Hi there,
I saw a similar issue but the responses did not help me solve the problem, so i thought i'd post as a new issue.
The program stops at assembling at contig k = 27. I tried with --kmin-1pass option but it didn't help. I thought maybe it was a memory issue so i capped that with “-m 0.5“, and that still did not fix the issue. I am running on a server where megahit comes complied and i just have to load the correct software as follows:
module load gcc/7.3.0 cuda/10.0.130 megahit/1.2.7
megahit -1 /home/path_to_forward_reads_/R1_P_trimmed.fq.gz -2 /home/path_to_reverse_reads_/R2_P_trimmed.fq.gz -m 0.5 -t 16 –k-min 27 –k-max 147 –k-step 10 -o /home/path_to_output_dir/assembly/_
I contacted the bioinformaticians that maintain the server but they said it does "Its Most likely this is caused by a problem with the code and so, I think contacting the megahit authors could be your best bet."
I get a large core file that i can attached but its >3GB, and here is the output of the log file:
2019-09-17 10:25:47 – MEGAHIT v1.2.7
2019-09-17 10:25:47 – Using megahit_core with POPCNT and BMI2 support
2019-09-17 10:25:47 – Convert reads to binary library
2019-09-17 10:25:47 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core buildlib /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib
2019-09-17 10:27:48 – INFO sequence/io/sequence_lib.cpp : 77 – Lib 0 (/home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/trimreads/SEEP_BRIDGE_DI_R1_P_trimmed.fq.gz,/home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/trimreads/SEEP_BRIDGE_DI_R2_P_trimmed.fq.gz): pe, 72595302 reads, 151 max length
2019-09-17 10:27:48 – INFO utils/utils.h : 152 – Real: 120.5771 user: 91.9506 sys: 21.9402 maxrss: 247472
2019-09-17 10:27:48 – Start assembly. Number of CPU threads 16
2019-09-17 10:27:48 – k list: 27,37,47,57,67,77,87,97,107,117,127,137,147
2019-09-17 10:27:48 – Memory used: 67537805312
2019-09-17 10:27:48 – Extract solid (k+1)-mers for k = 27
2019-09-17 10:27:48 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core count -k 27 -m 2 –host_mem 67537805312.0 –mem_flag 1 –output_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –num_cpu_threads 16 –read_lib_file /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/reads.lib
2019-09-17 10:27:48 – INFO sorting/base_engine.cpp : 148 – Preparing data…
2019-09-17 10:27:48 – INFO sequence/io/sequence_lib.cpp : 115 – Before reading, sizeof seq_package: 3215614856
2019-09-17 10:27:57 – INFO sequence/io/sequence_lib.cpp : 117 – After reading, sizeof seq_package: 3215614856
2019-09-17 10:27:57 – INFO sorting/kmer_counter.cpp : 76 – 72595302 reads, 151 max read length
2019-09-17 10:27:57 – INFO sorting/kmer_counter.cpp : 83 – 2 words per substring, 3 words per edge
2019-09-17 10:27:57 – INFO sorting/base_engine.cpp : 153 – Preparing data… Done. Time elapsed: 9.6948
2019-09-17 10:27:57 – INFO sorting/base_engine.cpp : 156 – Preparing partitions and calculating bucket sizes…
2019-09-17 10:28:08 – INFO sorting/base_engine.cpp : 80 – Minimum memory required: 4202744292 bytes
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 138 – Lv1 items: 1143937871, Lv2 items: 6283824
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 140 – Memory of derived class: 3887105048, Memory for Lv1+Lv2: 4676292668
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 168 – Preparing partitions and calculating bucket sizes… Done. Time elapsed: 13.4045
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 172 – Start main loop…
2019-09-17 10:28:11 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 0 to 1046
2019-09-17 10:28:24 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 12.8581
2019-09-17 10:28:40 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 16.9110
2019-09-17 10:28:40 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 1046 to 3148
2019-09-17 10:28:54 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 13.6388
2019-09-17 10:29:14 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 19.5220
2019-09-17 10:29:14 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 3148 to 6238
2019-09-17 10:29:28 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.1731
2019-09-17 10:29:49 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 21.2304
2019-09-17 10:29:49 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 6238 to 10512
2019-09-17 10:30:04 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.7469
2019-09-17 10:30:26 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 22.0881
2019-09-17 10:30:26 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 10512 to 16434
2019-09-17 10:30:41 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 15.2846
2019-09-17 10:31:04 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 23.1813
2019-09-17 10:31:04 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 16434 to 24991
2019-09-17 10:31:20 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 15.6392
2019-09-17 10:31:44 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 24.0282
2019-09-17 10:31:44 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 24991 to 39394
2019-09-17 10:32:00 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 16.1445
2019-09-17 10:32:26 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 25.6580
2019-09-17 10:32:26 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 39394 to 65536
2019-09-17 10:32:40 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 14.1519
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 16.3075
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 204 – Main loop done. Time elapsed: 285.5726
2019-09-17 10:32:56 – INFO sorting/base_engine.cpp : 207 – Postprocessing…
2019-09-17 10:33:00 – INFO sorting/kmer_counter.cpp : 406 – Total number of candidate reads: 4537891 (16253539)
2019-09-17 10:33:00 – INFO sorting/kmer_counter.cpp : 408 – Total number of solid edges: 948756888
2019-09-17 10:33:00 – INFO sorting/base_engine.cpp : 210 – Postprocess done. Time elapsed: 4.0569
2019-09-17 10:33:01 – INFO utils/utils.h : 152 – Real: 313.4382 user: 4613.5264 sys: 106.0754 maxrss: 8399168
2019-09-17 10:33:01 – Build graph for k = 27
2019-09-17 10:33:01 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core seq2sdbg –host_mem 67537805312.0 –mem_flag 1 –output_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –num_cpu_threads 16 -k 27 –kmer_from 0 –input_prefix /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 –need_mercy
2019-09-17 10:33:01 – INFO sorting/base_engine.cpp : 148 – Preparing data…
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 369 – Number edges: 948756888
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 415 – Bases to reserve: 33206491080, number contigs: 0, number multiplicity: 1185946110
2019-09-17 10:33:01 – INFO sorting/seq_to_sdbg.cpp : 422 – Before reading, sizeof seq_package: 8301622780, multiplicity vector: 1185946110
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 428 – Read 948756888 edges.
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 433 – After reading, sizeof seq_package: 8301622780/948756888/26565192864, multiplicity vector: 948756888/1185946110
2019-09-17 10:33:42 – INFO sorting/seq_to_sdbg.cpp : 440 – Adding mercy edges…
2019-09-17 10:34:04 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:05 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:06 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:08 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:09 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:10 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:11 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:13 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:15 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:16 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:17 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:18 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:20 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:21 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:22 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:23 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:24 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:26 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:27 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:28 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:29 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:31 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:32 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:33 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:34 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:36 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:37 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:38 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:39 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:41 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:42 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:43 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:44 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:46 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:47 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:48 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:49 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:51 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:52 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:53 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:54 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:56 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:57 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:58 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:34:59 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:01 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:02 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:03 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:04 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:05 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:07 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:08 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:09 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:10 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:12 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:13 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:14 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:15 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:17 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:18 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:19 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:20 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:22 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:23 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:24 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:25 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:27 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:28 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:29 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 65536 reads to search for mercy k-mers
2019-09-17 10:35:30 – INFO sorting/seq_to_sdbg.cpp : 192 – Read 15907 reads to search for mercy k-mers
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 356 – Number of reads: 4537891, Number of mercy edges: 137033696
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 444 – Done. Time elapsed: 108.5788
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 449 – After adding mercy, sizeof seq_package: 8301622780/1085790584/30402136352, multiplicity vector: 1085790584/1185946110
2019-09-17 10:35:31 – INFO sorting/seq_to_sdbg.cpp : 508 – Finally, sizeof seq_package: 8301622780/1085790584/30402136352, multiplicity vector: 1085790584/1185946110
2019-09-17 10:35:31 – INFO sorting/base_engine.cpp : 153 – Preparing data… Done. Time elapsed: 149.6824
2019-09-17 10:35:31 – INFO sorting/base_engine.cpp : 156 – Preparing partitions and calculating bucket sizes…
2019-09-17 10:35:40 – INFO sorting/base_engine.cpp : 80 – Minimum memory required: 11139101008 bytes
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 138 – Lv1 items: 868632467, Lv2 items: 4771536
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 140 – Memory of derived class: 10911031720, Memory for Lv1+Lv2: 3531788300
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 168 – Preparing partitions and calculating bucket sizes… Done. Time elapsed: 11.6378
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 172 – Start main loop…
2019-09-17 10:35:43 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 0 to 1575
2019-09-17 10:35:53 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 10.5633
2019-09-17 10:36:03 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.3918
2019-09-17 10:36:03 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 1575 to 4689
2019-09-17 10:36:10 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.6244
2019-09-17 10:36:21 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.8340
2019-09-17 10:36:21 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 4689 to 9223
2019-09-17 10:36:28 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.7369
2019-09-17 10:36:39 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.9330
2019-09-17 10:36:39 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 9223 to 15277
2019-09-17 10:36:46 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.9538
2019-09-17 10:36:57 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 10.9638
2019-09-17 10:36:57 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 15277 to 23201
2019-09-17 10:37:04 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.4609
2019-09-17 10:37:15 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.0484
2019-09-17 10:37:15 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 23201 to 33750
2019-09-17 10:37:23 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.4965
2019-09-17 10:37:34 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.1667
2019-09-17 10:37:34 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 33750 to 49499
2019-09-17 10:37:42 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 7.7935
2019-09-17 10:37:53 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 11.2160
2019-09-17 10:37:53 – INFO sorting/base_engine.cpp : 186 – Lv1 scanning from bucket 49499 to 65536
2019-09-17 10:37:59 – INFO sorting/base_engine.cpp : 193 – Lv1 scanning done. Large diff: 0. Time elapsed: 6.2833
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 199 – Lv1 fetching & sorting done. Time elapsed: 5.8518
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 204 – Main loop done. Time elapsed: 142.3261
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 207 – Postprocessing…
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 793 – Number of $ A C G T A- C- G- T-:
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 794 – 14742369 455415904 633657824 635116617 455152761 1084447 2405351 2421353 1067631
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 800 – Total number of edges: 2201064257
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 801 – Total number of ONEs: 2179343106
2019-09-17 10:38:05 – INFO sorting/seq_to_sdbg.cpp : 803 – Total number of $v edges: 14742369
2019-09-17 10:38:05 – INFO sorting/base_engine.cpp : 210 – Postprocess done. Time elapsed: 0.0642
2019-09-17 10:38:06 – INFO utils/utils.h : 152 – Real: 304.9620 user: 3416.7373 sys: 71.1459 maxrss: 13081104
2019-09-17 10:38:06 – Assemble contigs from SdBG for k = 27
2019-09-17 10:38:06 – command /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core assemble -s /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 -o /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/intermediate_contigs/k27 -t 16 –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
2019-09-17 10:38:53 – INFO main_assemble.cpp : 129 – Loading succinct de Bruijn graph: /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27Done. Time elapsed: 47.008568
2019-09-17 10:38:53 – INFO main_assemble.cpp : 133 – Number of Edges: 2201064257; K value: 27
2019-09-17 10:38:53 – INFO main_assemble.cpp : 140 – Number of CPU threads: 16
2019-09-17 10:39:20 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 2; Accumulated tips removed: 368650; time elapsed: 2.6854
2019-09-17 10:39:25 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 4; Accumulated tips removed: 1100561; time elapsed: 4.6705
2019-09-17 10:39:35 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 8; Accumulated tips removed: 2089344; time elapsed: 10.1763
2019-09-17 10:39:57 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 16; Accumulated tips removed: 3621395; time elapsed: 21.7634
2019-09-17 10:40:37 – INFO assembly/sdbg_pruning.cpp : 160 – Removing tips with length less than 32; Accumulated tips removed: 5806553; time elapsed: 39.9274
2019-09-17 10:41:33 – INFO assembly/sdbg_pruning.cpp : 169 – Removing tips with length less than 54; Accumulated tips removed: 7829599; time elapsed: 56.6510
2019-09-17 10:41:33 – INFO main_assemble.cpp : 158 – Tips removal done! Time elapsed(sec): 160.040
2019-09-17 10:45:02 – INFO assembly/unitig_graph.cpp : 84 – Graph size without loops: 12073549, palindrome: 1500
2019-09-17 10:45:12 – INFO main_assemble.cpp : 167 – unitig graph size: 12085257, time for building: 218.576
2019-09-17 10:45:32 – INFO assembly/contig_stat.h : 40 – Max: 23761, Min: 28, N50: 147, number contigs: 12085257, number isolated: 3153332, number looped: 11708, total size: 1332397452,
2019-09-17 10:45:32 – INFO main_assemble.cpp : 184 – Graph cleaning round 1
2019-09-17 10:45:47 – INFO main_assemble.cpp : 201 – Number of bubbles removed: 727321, Time elapsed(sec): 14.906
2019-09-17 10:45:56 – INFO main_assemble.cpp : 211 – Number of complex bubbles removed: 219193, Time elapsed(sec): 9.180119
2019-09-17 10:45:59 – INFO main_assemble.cpp : 222 – Number unitigs disconnected: 591974, time: 2.664
2019-09-17 10:46:00 – INFO main_assemble.cpp : 246 – Unitigs removed in excessive pruning: 808, time: 1.403
2019-09-17 10:46:00 – INFO main_assemble.cpp : 184 – Graph cleaning round 2
2019-09-17 10:46:07 – INFO main_assemble.cpp : 192 – Tips removed: 127963, time: 6.796
2019-09-17 10:46:09 – megahit_core: /dev/shm/ebuser/avx2/MEGAHIT/1.2.7/gmklc-2018.3.100/megahit-1.2.7/src/assembly/unitig_graph.cpp:315: void UnitigGraph::Refresh(bool): Assertion `!(next_adapter.GetFlag() & kDeleted)’ failed.
2019-09-17 10:46:30 – Error occurs, please refer to /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/log for detail
2019-09-17 10:46:30 – Command: /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/gcc7.3/cuda10.0/megahit/1.2.7/bin/megahit_core assemble -s /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/tmp/k27/27 -o /home/sacrowe/projects/def-sacrowe/sacrowe/HK_Fe_Seep/assembly/Seep_bridge/intermediate_contigs/k27 -t 16 –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 -6
In the mean time i have assembled this sample locally on my own workstation - so it something to do with it being on a server? Any thoughts much appreciated.
Thanks!
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