Open clb21565 opened 3 years ago
Dear all, our lab loves MEGAHIT. :-]
I am attempting to assemble a rather large dataset but run into a consistent error at the local assembly step. Please see the below log file: 2021-02-07 11:51:31 - MEGAHIT v1.2.9 2021-02-07 11:51:31 - Using megahit_core with POPCNT and BMI2 support 2021-02-07 11:51:31 - Convert reads to binary library 2021-02-07 11:51:31 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core buildlib /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib 2021-02-07 12:41:08 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/work/cascades/clb21565/WW_Analysis/hsp/data/merged/merged.fq): interleaved, 3501961168 reads, 151 max length' 2021-02-07 12:41:08 - b'INFO utils/utils.h : 152 - Real: 2976.4287\tuser: 2790.0804\tsys: 784.2864\tmaxrss: 268108' 2021-02-07 12:41:08 - k-max reset to: 127 2021-02-07 12:41:08 - Start assembly. Number of CPU threads 32 2021-02-07 12:41:08 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-07 12:41:08 - Memory used: 2921768228044 2021-02-07 12:41:08 - Extracting solid (k+1)-mers and building sdbg for k = 27 2021-02-07 12:41:08 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core read2sdbg -k 27 -m 1 --host_mem 2921768228044 --mem_flag 1 --output_prefix /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27 --num_cpu_threads 32 --read_lib_file /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib 2021-02-07 12:41:08 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-07 12:47:13 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 105 - 3501961168 reads, 151 max read length, 476462616690 total bases' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 109 - 2 words per substring' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 124 - Number of files for mercy candidate reads: 64' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 148 - Preparing data...' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s2.cpp : 103 - 2 words per substring, words per dummy node ($v): 2' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 153 - Preparing data... Done. Time elapsed: 0.0055' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 156 - Preparing partitions and calculating bucket sizes...' 2021-02-07 12:51:01 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory required: 177079766092 bytes' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items: 103757934318, Lv2 items: 1139918688' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 140 - Memory of derived class: 150853707752, Memory for Lv1+Lv2: 424151086776' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 168 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 344.9476' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 172 - Start main loop...' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 0 to 1593' 2021-02-07 12:57:47 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 280.0469' 2021-02-07 13:13:58 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 970.8637' 2021-02-07 13:13:58 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 1593 to 4791' 2021-02-07 13:19:19 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 320.8224' 2021-02-07 13:39:13 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1194.4518' 2021-02-07 13:39:13 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 4791 to 9556' 2021-02-07 13:44:47 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 333.9242' 2021-02-07 14:06:26 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1299.1801' 2021-02-07 14:06:26 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 9556 to 15953' 2021-02-07 14:12:15 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 349.1602' 2021-02-07 14:34:57 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1361.3803' 2021-02-07 14:34:57 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 15953 to 24268' 2021-02-07 14:40:50 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 353.1718' 2021-02-07 15:03:23 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1353.4250' 2021-02-07 15:03:23 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 24268 to 35202' 2021-02-07 15:09:29 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 365.5283' 2021-02-07 15:32:31 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1382.5520' 2021-02-07 15:32:31 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 35202 to 51037' 2021-02-07 15:38:44 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 372.9404' 2021-02-07 16:02:09 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1404.8432' 2021-02-07 16:02:09 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 51037 to 65536' 2021-02-07 16:06:56 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 286.9658' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 713.0240' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 204 - Main loop done. Time elapsed: 12342.2821' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 207 - Postprocessing...' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 618 - Number of $ A C G T A- C- G- T-:' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 619 - 562232990 22120957225 26525195129 26715977585 22197884375 295338486 428129073 429298387 293555446' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 624 - Total number of edges: 99568568696' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 625 - Total number of ONEs: 97560014314' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 627 - Total number of $v edges: 562232990' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 210 - Postprocess done. Time elapsed: 0.0782' 2021-02-07 16:18:52 - b'INFO utils/utils.h : 152 - Real: 13064.2568\tuser: 394516.6393\tsys: 1170.5182\tmaxrss: 561615940' 2021-02-07 16:18:52 - Assemble contigs from SdBG for k = 27 2021-02-07 16:18:52 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core assemble -s /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27 -t 32 --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 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 129 - Loading succinct de Bruijn graph: /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27Done. Time elapsed: 1416.280805' 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 133 - Number of Edges: 99568568696; K value: 27' 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 140 - Number of CPU threads: 32' 2021-02-07 16:50:08 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 2; Accumulated tips removed: 36511936; time elapsed: 44.9818' 2021-02-07 16:51:47 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 4; Accumulated tips removed: 85813836; time elapsed: 98.4318' 2021-02-07 16:55:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 8; Accumulated tips removed: 174561972; time elapsed: 238.3606' 2021-02-07 17:05:25 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 16; Accumulated tips removed: 326254208; time elapsed: 580.2081' 2021-02-07 17:23:04 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 32; Accumulated tips removed: 525776940; time elapsed: 1058.3651' 2021-02-07 17:45:34 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips with length less than 54; Accumulated tips removed: 606218047; time elapsed: 1349.9091' 2021-02-07 17:45:34 - b'INFO main_assemble.cpp : 158 - Tips removal done! Time elapsed(sec): 3785.370' 2021-02-07 21:46:42 - b'INFO assembly/unitig_graph.cpp : 84 - Graph size without loops: 1680992444, palindrome: 66885' 2021-02-07 21:57:38 - b'INFO main_assemble.cpp : 167 - unitig graph size: 1681019835, time for building: 15124.842' 2021-02-08 00:51:52 - b'INFO assembly/contig_stat.h : 40 - Max: 3192, Min: 28, N50: 55, number contigs: 1681019835, number isolated: 61827410, number looped: 27391, total size: 89577034100,' 2021-02-08 00:51:52 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 1' 2021-02-08 01:05:34 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 38996058, Time elapsed(sec): 822.519' 2021-02-08 01:16:16 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 8585891, Time elapsed(sec): 641.904775' 2021-02-08 01:51:45 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 603225070, time: 2128.630' 2021-02-08 01:55:26 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 2355383, time: 221.613' 2021-02-08 01:55:26 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 2' 2021-02-08 02:16:03 - b'INFO main_assemble.cpp : 192 - Tips removed: 203571270, time: 1236.444' 2021-02-08 02:20:40 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 5472143, Time elapsed(sec): 277.009' 2021-02-08 02:25:24 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 1882859, Time elapsed(sec): 284.254417' 2021-02-08 02:28:33 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 1809067, time: 188.936' 2021-02-08 02:30:49 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 189024, time: 136.217' 2021-02-08 02:30:49 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 3' 2021-02-08 02:40:32 - b'INFO main_assemble.cpp : 192 - Tips removed: 472614, time: 583.387' 2021-02-08 02:43:38 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 59629, Time elapsed(sec): 185.293' 2021-02-08 02:47:21 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 32125, Time elapsed(sec): 223.323568' 2021-02-08 02:49:55 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 138373, time: 153.962' 2021-02-08 02:52:04 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 32906, time: 129.207' 2021-02-08 02:52:04 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 4' 2021-02-08 03:01:11 - b'INFO main_assemble.cpp : 192 - Tips removed: 39252, time: 547.200' 2021-02-08 03:04:16 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 6039, Time elapsed(sec): 184.673' 2021-02-08 03:07:54 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 1924, Time elapsed(sec): 217.650283' 2021-02-08 03:10:26 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 26952, time: 152.135' 2021-02-08 03:12:33 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 7306, time: 127.341' 2021-02-08 03:12:33 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 5' 2021-02-08 03:21:28 - b'INFO main_assemble.cpp : 192 - Tips removed: 5973, time: 534.961' 2021-02-08 03:24:26 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 1224, Time elapsed(sec): 177.597' 2021-02-08 03:27:58 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 336, Time elapsed(sec): 212.630321' 2021-02-08 03:30:27 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 9037, time: 148.827' 2021-02-08 03:32:35 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 1860, time: 128.013' 2021-02-08 04:58:11 - b'INFO assembly/contig_stat.h : 40 - Max: 163220, Min: 28, N50: 94, number contigs: 809904421, number isolated: 117218086, number looped: 27861, total size: 58973968165,' 2021-02-08 05:40:53 - b'INFO main_assemble.cpp : 267 - Time to output: 2561.678896' 2021-02-08 08:41:09 - b'INFO main_assemble.cpp : 289 - Number of local low depth unitigs removed: 37769867, complex bubbles removed: 3122295, time: 10816.279127' 2021-02-08 09:55:41 - b'INFO assembly/contig_stat.h : 40 - Max: 163268, Min: 28, N50: 107, number contigs: 704498991, number isolated: 118302409, number looped: 29723, total size: 55148629847,' 2021-02-08 10:34:34 - b'INFO utils/utils.h : 152 - Real: 65741.9437\tuser: 1836326.9823\tsys: 8103.8959\tmaxrss: 284596600' 2021-02-08 10:34:34 - Local assembly for k = 27 2021-02-08 10:34:34 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 12:35:56 - b'INFO localasm/hash_mapper.cpp : 100 - Number of contigs: 34647749, index size: 1439936128' 2021-02-08 12:35:56 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper construction time elapsed: 7282.539679' 2021-02-08 12:35:56 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-08 12:40:20 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-08 12:40:20 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time elapsed: 263.341237' 2021-02-08 12:40:21 - b'INFO localasm/local_assemble.cpp : 134 - Lib 0, insert size: 162.00 sd: 72.69' 2021-02-08 12:40:21 - b'INFO localasm/local_assemble.cpp : 330 - Insert size estimation time elapsed: 0.941624' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 221 - Lib 0: total 3501961168 reads, aligned 1803593334, added 529796980 reads to local assembly' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time elapsed: 1626.835557' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number of reads to do local assembly: 2' 2021-02-08 13:07:28 - b'[ERROR] Cannot open /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa. Now exit to system...' 2021-02-08 13:07:38 - Error occurs, please refer to /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/all_merged.log for detail 2021-02-08 13:07:38 - Command: /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37; Exit code 255 2021-02-08 13:41:07 - MEGAHIT v1.2.9 2021-02-08 13:41:07 - Using megahit_core with POPCNT and BMI2 support 2021-02-08 13:41:07 - passing check point 0 2021-02-08 13:41:07 - passing check point 1 2021-02-08 13:41:07 - k-max reset to: 127 2021-02-08 13:41:07 - Start assembly. Number of CPU threads 32 2021-02-08 13:41:07 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-08 13:41:07 - Memory used: 2921768228044 2021-02-08 13:41:07 - passing check point 2 2021-02-08 13:41:07 - passing check point 3 2021-02-08 13:41:07 - Local assembly for k = 27 2021-02-08 13:41:07 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 14:21:02 - MEGAHIT v1.2.9 2021-02-08 14:21:02 - Using megahit_core with POPCNT and BMI2 support 2021-02-08 14:21:02 - passing check point 0 2021-02-08 14:21:02 - passing check point 1 2021-02-08 14:21:02 - k-max reset to: 127 2021-02-08 14:21:02 - Start assembly. Number of CPU threads 32 2021-02-08 14:21:02 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-08 14:21:02 - Memory used: 121405936435 2021-02-08 14:21:02 - passing check point 2 2021-02-08 14:21:02 - passing check point 3 2021-02-08 14:21:02 - Local assembly for k = 27 2021-02-08 14:21:02 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 15:35:26 - b'INFO localasm/hash_mapper.cpp : 100 - Number of contigs: 34647749, index size: 1439936128' 2021-02-08 15:35:26 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper construction time elapsed: 6859.373239' 2021-02-08 15:35:26 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-08 15:39:51 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-08 15:39:51 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time elapsed: 264.648560' 2021-02-08 15:39:52 - b'INFO localasm/local_assemble.cpp : 134 - Lib 0, insert size: 162.00 sd: 72.69' 2021-02-08 15:39:52 - b'INFO localasm/local_assemble.cpp : 330 - Insert size estimation time elapsed: 0.999625' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 221 - Lib 0: total 3501961168 reads, aligned 1803593334, added 529796980 reads to local assembly' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time elapsed: 1625.172149' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number of reads to do local assembly: 2' 2021-02-08 16:07:01 - b'[ERROR] Cannot open /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa. Now exit to system...' 2021-02-08 16:07:11 - Error occurs, please refer to /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/all_merged.log for detail 2021-02-08 16:07:11 - Command: /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37; Exit code 255 2021-02-09 10:30:51 - MEGAHIT v1.2.9 2021-02-09 10:30:51 - Using megahit_core with POPCNT and BMI2 support 2021-02-09 10:30:51 - passing check point 0 2021-02-09 10:30:51 - passing check point 1 2021-02-09 10:30:51 - k-max reset to: 127 2021-02-09 10:30:51 - Start assembly. Number of CPU threads 32 2021-02-09 10:30:51 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-09 10:30:51 - Memory used: 2921768228044 2021-02-09 10:30:51 - passing check point 2 2021-02-09 10:30:51 - passing check point 3 2021-02-09 10:30:51 - Local assembly for k = 27 2021-02-09 10:30:51 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37
Any guidance would be very much appreciated!
Dear all, our lab loves MEGAHIT. :-]
I am attempting to assemble a rather large dataset but run into a consistent error at the local assembly step. Please see the below log file: 2021-02-07 11:51:31 - MEGAHIT v1.2.9 2021-02-07 11:51:31 - Using megahit_core with POPCNT and BMI2 support 2021-02-07 11:51:31 - Convert reads to binary library 2021-02-07 11:51:31 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core buildlib /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib 2021-02-07 12:41:08 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/work/cascades/clb21565/WW_Analysis/hsp/data/merged/merged.fq): interleaved, 3501961168 reads, 151 max length' 2021-02-07 12:41:08 - b'INFO utils/utils.h : 152 - Real: 2976.4287\tuser: 2790.0804\tsys: 784.2864\tmaxrss: 268108' 2021-02-07 12:41:08 - k-max reset to: 127 2021-02-07 12:41:08 - Start assembly. Number of CPU threads 32 2021-02-07 12:41:08 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-07 12:41:08 - Memory used: 2921768228044 2021-02-07 12:41:08 - Extracting solid (k+1)-mers and building sdbg for k = 27 2021-02-07 12:41:08 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core read2sdbg -k 27 -m 1 --host_mem 2921768228044 --mem_flag 1 --output_prefix /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27 --num_cpu_threads 32 --read_lib_file /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib 2021-02-07 12:41:08 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-07 12:47:13 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 105 - 3501961168 reads, 151 max read length, 476462616690 total bases' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 109 - 2 words per substring' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s1.cpp : 124 - Number of files for mercy candidate reads: 64' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 148 - Preparing data...' 2021-02-07 12:47:22 - b'INFO sorting/read_to_sdbg_s2.cpp : 103 - 2 words per substring, words per dummy node ($v): 2' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 153 - Preparing data... Done. Time elapsed: 0.0055' 2021-02-07 12:47:22 - b'INFO sorting/base_engine.cpp : 156 - Preparing partitions and calculating bucket sizes...' 2021-02-07 12:51:01 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory required: 177079766092 bytes' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items: 103757934318, Lv2 items: 1139918688' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 140 - Memory of derived class: 150853707752, Memory for Lv1+Lv2: 424151086776' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 168 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 344.9476' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 172 - Start main loop...' 2021-02-07 12:53:07 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 0 to 1593' 2021-02-07 12:57:47 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 280.0469' 2021-02-07 13:13:58 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 970.8637' 2021-02-07 13:13:58 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 1593 to 4791' 2021-02-07 13:19:19 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 320.8224' 2021-02-07 13:39:13 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1194.4518' 2021-02-07 13:39:13 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 4791 to 9556' 2021-02-07 13:44:47 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 333.9242' 2021-02-07 14:06:26 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1299.1801' 2021-02-07 14:06:26 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 9556 to 15953' 2021-02-07 14:12:15 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 349.1602' 2021-02-07 14:34:57 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1361.3803' 2021-02-07 14:34:57 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 15953 to 24268' 2021-02-07 14:40:50 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 353.1718' 2021-02-07 15:03:23 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1353.4250' 2021-02-07 15:03:23 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 24268 to 35202' 2021-02-07 15:09:29 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 365.5283' 2021-02-07 15:32:31 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1382.5520' 2021-02-07 15:32:31 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 35202 to 51037' 2021-02-07 15:38:44 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 372.9404' 2021-02-07 16:02:09 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 1404.8432' 2021-02-07 16:02:09 - b'INFO sorting/base_engine.cpp : 186 - Lv1 scanning from bucket 51037 to 65536' 2021-02-07 16:06:56 - b'INFO sorting/base_engine.cpp : 193 - Lv1 scanning done. Large diff: 0. Time elapsed: 286.9658' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 199 - Lv1 fetching & sorting done. Time elapsed: 713.0240' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 204 - Main loop done. Time elapsed: 12342.2821' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 207 - Postprocessing...' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 618 - Number of $ A C G T A- C- G- T-:' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 619 - 562232990 22120957225 26525195129 26715977585 22197884375 295338486 428129073 429298387 293555446' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 624 - Total number of edges: 99568568696' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 625 - Total number of ONEs: 97560014314' 2021-02-07 16:18:49 - b'INFO sorting/read_to_sdbg_s2.cpp : 627 - Total number of $v edges: 562232990' 2021-02-07 16:18:49 - b'INFO sorting/base_engine.cpp : 210 - Postprocess done. Time elapsed: 0.0782' 2021-02-07 16:18:52 - b'INFO utils/utils.h : 152 - Real: 13064.2568\tuser: 394516.6393\tsys: 1170.5182\tmaxrss: 561615940' 2021-02-07 16:18:52 - Assemble contigs from SdBG for k = 27 2021-02-07 16:18:52 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core assemble -s /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27 -t 32 --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 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 129 - Loading succinct de Bruijn graph: /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/k27/27Done. Time elapsed: 1416.280805' 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 133 - Number of Edges: 99568568696; K value: 27' 2021-02-07 16:42:28 - b'INFO main_assemble.cpp : 140 - Number of CPU threads: 32' 2021-02-07 16:50:08 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 2; Accumulated tips removed: 36511936; time elapsed: 44.9818' 2021-02-07 16:51:47 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 4; Accumulated tips removed: 85813836; time elapsed: 98.4318' 2021-02-07 16:55:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 8; Accumulated tips removed: 174561972; time elapsed: 238.3606' 2021-02-07 17:05:25 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 16; Accumulated tips removed: 326254208; time elapsed: 580.2081' 2021-02-07 17:23:04 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 32; Accumulated tips removed: 525776940; time elapsed: 1058.3651' 2021-02-07 17:45:34 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips with length less than 54; Accumulated tips removed: 606218047; time elapsed: 1349.9091' 2021-02-07 17:45:34 - b'INFO main_assemble.cpp : 158 - Tips removal done! Time elapsed(sec): 3785.370' 2021-02-07 21:46:42 - b'INFO assembly/unitig_graph.cpp : 84 - Graph size without loops: 1680992444, palindrome: 66885' 2021-02-07 21:57:38 - b'INFO main_assemble.cpp : 167 - unitig graph size: 1681019835, time for building: 15124.842' 2021-02-08 00:51:52 - b'INFO assembly/contig_stat.h : 40 - Max: 3192, Min: 28, N50: 55, number contigs: 1681019835, number isolated: 61827410, number looped: 27391, total size: 89577034100,' 2021-02-08 00:51:52 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 1' 2021-02-08 01:05:34 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 38996058, Time elapsed(sec): 822.519' 2021-02-08 01:16:16 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 8585891, Time elapsed(sec): 641.904775' 2021-02-08 01:51:45 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 603225070, time: 2128.630' 2021-02-08 01:55:26 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 2355383, time: 221.613' 2021-02-08 01:55:26 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 2' 2021-02-08 02:16:03 - b'INFO main_assemble.cpp : 192 - Tips removed: 203571270, time: 1236.444' 2021-02-08 02:20:40 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 5472143, Time elapsed(sec): 277.009' 2021-02-08 02:25:24 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 1882859, Time elapsed(sec): 284.254417' 2021-02-08 02:28:33 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 1809067, time: 188.936' 2021-02-08 02:30:49 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 189024, time: 136.217' 2021-02-08 02:30:49 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 3' 2021-02-08 02:40:32 - b'INFO main_assemble.cpp : 192 - Tips removed: 472614, time: 583.387' 2021-02-08 02:43:38 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 59629, Time elapsed(sec): 185.293' 2021-02-08 02:47:21 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 32125, Time elapsed(sec): 223.323568' 2021-02-08 02:49:55 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 138373, time: 153.962' 2021-02-08 02:52:04 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 32906, time: 129.207' 2021-02-08 02:52:04 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 4' 2021-02-08 03:01:11 - b'INFO main_assemble.cpp : 192 - Tips removed: 39252, time: 547.200' 2021-02-08 03:04:16 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 6039, Time elapsed(sec): 184.673' 2021-02-08 03:07:54 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 1924, Time elapsed(sec): 217.650283' 2021-02-08 03:10:26 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 26952, time: 152.135' 2021-02-08 03:12:33 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 7306, time: 127.341' 2021-02-08 03:12:33 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 5' 2021-02-08 03:21:28 - b'INFO main_assemble.cpp : 192 - Tips removed: 5973, time: 534.961' 2021-02-08 03:24:26 - b'INFO main_assemble.cpp : 201 - Number of bubbles removed: 1224, Time elapsed(sec): 177.597' 2021-02-08 03:27:58 - b'INFO main_assemble.cpp : 211 - Number of complex bubbles removed: 336, Time elapsed(sec): 212.630321' 2021-02-08 03:30:27 - b'INFO main_assemble.cpp : 222 - Number unitigs disconnected: 9037, time: 148.827' 2021-02-08 03:32:35 - b'INFO main_assemble.cpp : 246 - Unitigs removed in excessive pruning: 1860, time: 128.013' 2021-02-08 04:58:11 - b'INFO assembly/contig_stat.h : 40 - Max: 163220, Min: 28, N50: 94, number contigs: 809904421, number isolated: 117218086, number looped: 27861, total size: 58973968165,' 2021-02-08 05:40:53 - b'INFO main_assemble.cpp : 267 - Time to output: 2561.678896' 2021-02-08 08:41:09 - b'INFO main_assemble.cpp : 289 - Number of local low depth unitigs removed: 37769867, complex bubbles removed: 3122295, time: 10816.279127' 2021-02-08 09:55:41 - b'INFO assembly/contig_stat.h : 40 - Max: 163268, Min: 28, N50: 107, number contigs: 704498991, number isolated: 118302409, number looped: 29723, total size: 55148629847,' 2021-02-08 10:34:34 - b'INFO utils/utils.h : 152 - Real: 65741.9437\tuser: 1836326.9823\tsys: 8103.8959\tmaxrss: 284596600' 2021-02-08 10:34:34 - Local assembly for k = 27 2021-02-08 10:34:34 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 12:35:56 - b'INFO localasm/hash_mapper.cpp : 100 - Number of contigs: 34647749, index size: 1439936128' 2021-02-08 12:35:56 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper construction time elapsed: 7282.539679' 2021-02-08 12:35:56 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-08 12:40:20 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-08 12:40:20 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time elapsed: 263.341237' 2021-02-08 12:40:21 - b'INFO localasm/local_assemble.cpp : 134 - Lib 0, insert size: 162.00 sd: 72.69' 2021-02-08 12:40:21 - b'INFO localasm/local_assemble.cpp : 330 - Insert size estimation time elapsed: 0.941624' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 221 - Lib 0: total 3501961168 reads, aligned 1803593334, added 529796980 reads to local assembly' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time elapsed: 1626.835557' 2021-02-08 13:07:28 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number of reads to do local assembly: 2' 2021-02-08 13:07:28 - b'[ERROR] Cannot open /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa. Now exit to system...' 2021-02-08 13:07:38 - Error occurs, please refer to /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/all_merged.log for detail 2021-02-08 13:07:38 - Command: /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37; Exit code 255 2021-02-08 13:41:07 - MEGAHIT v1.2.9 2021-02-08 13:41:07 - Using megahit_core with POPCNT and BMI2 support 2021-02-08 13:41:07 - passing check point 0 2021-02-08 13:41:07 - passing check point 1 2021-02-08 13:41:07 - k-max reset to: 127 2021-02-08 13:41:07 - Start assembly. Number of CPU threads 32 2021-02-08 13:41:07 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-08 13:41:07 - Memory used: 2921768228044 2021-02-08 13:41:07 - passing check point 2 2021-02-08 13:41:07 - passing check point 3 2021-02-08 13:41:07 - Local assembly for k = 27 2021-02-08 13:41:07 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 14:21:02 - MEGAHIT v1.2.9 2021-02-08 14:21:02 - Using megahit_core with POPCNT and BMI2 support 2021-02-08 14:21:02 - passing check point 0 2021-02-08 14:21:02 - passing check point 1 2021-02-08 14:21:02 - k-max reset to: 127 2021-02-08 14:21:02 - Start assembly. Number of CPU threads 32 2021-02-08 14:21:02 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-08 14:21:02 - Memory used: 121405936435 2021-02-08 14:21:02 - passing check point 2 2021-02-08 14:21:02 - passing check point 3 2021-02-08 14:21:02 - Local assembly for k = 27 2021-02-08 14:21:02 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37 2021-02-08 15:35:26 - b'INFO localasm/hash_mapper.cpp : 100 - Number of contigs: 34647749, index size: 1439936128' 2021-02-08 15:35:26 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper construction time elapsed: 6859.373239' 2021-02-08 15:35:26 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 147131343528' 2021-02-08 15:39:51 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 147131343528' 2021-02-08 15:39:51 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time elapsed: 264.648560' 2021-02-08 15:39:52 - b'INFO localasm/local_assemble.cpp : 134 - Lib 0, insert size: 162.00 sd: 72.69' 2021-02-08 15:39:52 - b'INFO localasm/local_assemble.cpp : 330 - Insert size estimation time elapsed: 0.999625' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 221 - Lib 0: total 3501961168 reads, aligned 1803593334, added 529796980 reads to local assembly' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time elapsed: 1625.172149' 2021-02-08 16:06:57 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number of reads to do local assembly: 2' 2021-02-08 16:07:01 - b'[ERROR] Cannot open /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa. Now exit to system...' 2021-02-08 16:07:11 - Error occurs, please refer to /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/all_merged.log for detail 2021-02-08 16:07:11 - Command: /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37; Exit code 255 2021-02-09 10:30:51 - MEGAHIT v1.2.9 2021-02-09 10:30:51 - Using megahit_core with POPCNT and BMI2 support 2021-02-09 10:30:51 - passing check point 0 2021-02-09 10:30:51 - passing check point 1 2021-02-09 10:30:51 - k-max reset to: 127 2021-02-09 10:30:51 - Start assembly. Number of CPU threads 32 2021-02-09 10:30:51 - k list: 27,37,47,57,67,77,87,97,107,117,127 2021-02-09 10:30:51 - Memory used: 2921768228044 2021-02-09 10:30:51 - passing check point 2 2021-02-09 10:30:51 - passing check point 3 2021-02-09 10:30:51 - Local assembly for k = 27 2021-02-09 10:30:51 - command /home/clb21565/miniconda3/envs/megahit/bin/megahit_core local -c /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.contigs.fa -l /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/tmp/reads.lib -t 32 -o /work/cascades/clb21565/WW_Analysis/hsp/assemblies/all/intermediate_contigs/k27.local.fa --kmax 37
Any guidance would be very much appreciated!