2024-12-08 20:39:55 - MEGAHIT v1.2.

9
2024-12-08 20:39:55 - Using megahit_core with POPCNT and BMI2 support
2024-12-08 20:39:55 - Convert reads to binary library
2024-12-08 20:39:55 - command /opt/conda/bin/megahit_core buildlib
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib
2024-12-08 20:39:56 - b'INFO sequence/io/sequence_lib.cpp : 75 - Lib 0
(/data/input.fastq): se, 1546943 reads, 45 max length'
2024-12-08 20:39:56 - b'INFO utils/utils.h : 152 - Real: 1.3934\
tuser: 1.1590\tsys: 0.1623\tmaxrss: 48728'
2024-12-08 20:39:56 - k-max reset to: 59
2024-12-08 20:39:56 - Start assembly. Number of CPU threads 6
2024-12-08 20:39:56 - k list: 21,29,39,59
2024-12-08 20:39:56 - Memory used: 29961916416
2024-12-08 20:39:56 - Extract solid (k+1)-mers for k = 21
2024-12-08 20:39:56 - command /opt/conda/bin/megahit_core count -k 21 -m 2 --
host_mem 29961916416 --mem_flag 1 --output_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k21/21 --num_cpu_threads 6 --read_lib_file
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib
2024-12-08 20:39:56 - b'INFO sorting/base_engine.cpp : 148 - Preparing
data...'
2024-12-08 20:39:56 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before
reading, sizeof seq_package: 29757156'
2024-12-08 20:39:56 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading,
sizeof seq_package: 29757156'
2024-12-08 20:39:56 - b'INFO sorting/kmer_counter.cpp : 76 - 1546943 reads,
45 max read length'
2024-12-08 20:39:56 - b'INFO sorting/kmer_counter.cpp : 82 - 2 words per
substring, 2 words per edge'
2024-12-08 20:39:56 - b'INFO sorting/base_engine.cpp : 153 - Preparing
data... Done. Time elapsed: 0.1689'
2024-12-08 20:39:56 - b'INFO sorting/base_engine.cpp : 156 - Preparing
partitions and calculating bucket sizes...'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory
required: 47378708 bytes'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items:
4938817, Lv2 items: 24688'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 139 - Memory of
derived class: 45821628, Memory for Lv1+Lv2: 20150276'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 165 - Preparing
partitions and calculating bucket sizes... Done. Time elapsed: 0.7475'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 172 - Start main
loop...'
2024-12-08 20:39:57 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 0 to 1144'
2024-12-08 20:39:58 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.9620'
2024-12-08 20:39:59 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.9046'
2024-12-08 20:39:59 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 1144 to 3386'
2024-12-08 20:40:00 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.0164'
2024-12-08 20:40:01 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.1710'
2024-12-08 20:40:01 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 3386 to 6714'
2024-12-08 20:40:02 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.1160'
2024-12-08 20:40:03 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.0868'
2024-12-08 20:40:03 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 6714 to 11428'
2024-12-08 20:40:04 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.0759'
2024-12-08 20:40:06 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.4161'
2024-12-08 20:40:06 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 11428 to 17905'
2024-12-08 20:40:07 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.2922'
2024-12-08 20:40:09 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.5337'
2024-12-08 20:40:09 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 17905 to 27076'
2024-12-08 20:40:10 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.1297'
2024-12-08 20:40:11 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.3457'
2024-12-08 20:40:11 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 27076 to 42425'
2024-12-08 20:40:12 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.9537'
2024-12-08 20:40:13 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 1.2810'
2024-12-08 20:40:13 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 42425 to 65536'
2024-12-08 20:40:14 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 1.0669'
2024-12-08 20:40:15 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.8300'
2024-12-08 20:40:15 - b'INFO sorting/base_engine.cpp : 204 - Main loop
done. Time elapsed: 18.1902'
2024-12-08 20:40:15 - b'INFO sorting/base_engine.cpp : 207 -
Postprocessing...'
2024-12-08 20:40:15 - b'INFO sorting/kmer_counter.cpp : 405 - Total number
of candidate reads: 30634 (122644)'
2024-12-08 20:40:15 - b'INFO sorting/kmer_counter.cpp : 407 - Total number
of solid edges: 2905097'
2024-12-08 20:40:16 - b'INFO sorting/base_engine.cpp : 210 - Postprocess
done. Time elapsed: 0.3458'
2024-12-08 20:40:16 - b'INFO utils/utils.h : 152 - Real: 19.4691\
tuser: 26.0636\tsys: 0.2607\tmaxrss: 83124'
2024-12-08 20:40:16 - Build graph for k = 21
2024-12-08 20:40:16 - command /opt/conda/bin/megahit_core seq2sdbg --host_mem
29961916416 --mem_flag 1 --output_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k21/21 --num_cpu_threads 6 -k 21 --kmer_from 0
--input_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k21/21 --need_mercy
2024-12-08 20:40:16 - b'INFO sorting/base_engine.cpp : 148 - Preparing
data...'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 369 - Number edges:
2905097'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 413 - Bases to
reserve: 79890162, number contigs: 0, number multiplicity: 3631371'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 421 - Before
reading, sizeof seq_package: 19972552, multiplicity vector: 3631371'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 428 - Read 2905097
edges.'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 429 - After reading,
sizeof seq_package: 19972552/2905097/63912134, multiplicity vector:
2905097/3631371'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 440 - Adding mercy
edges...'
2024-12-08 20:40:16 - b'INFO sorting/seq_to_sdbg.cpp : 191 - Read 30634
reads to search for mercy k-mers'
2024-12-08 20:40:17 - b'INFO sorting/seq_to_sdbg.cpp : 355 - Number of
reads: 30634, Number of mercy edges: 186125'
2024-12-08 20:40:17 - b'INFO sorting/seq_to_sdbg.cpp : 444 - Done. Time
elapsed: 0.9659'
2024-12-08 20:40:17 - b'INFO sorting/seq_to_sdbg.cpp : 445 - After adding
mercy, sizeof seq_package: 19972552/3091222/68006884, multiplicity vector:
3091222/3631371'
2024-12-08 20:40:17 - b'INFO sorting/seq_to_sdbg.cpp : 506 - Finally,
sizeof seq_package: 19972552/3091222/68006884, multiplicity vector:
3091222/3631371'
2024-12-08 20:40:17 - b'INFO sorting/base_engine.cpp : 153 - Preparing
data... Done. Time elapsed: 1.6128'
2024-12-08 20:40:17 - b'INFO sorting/base_engine.cpp : 156 - Preparing
partitions and calculating bucket sizes...'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory
required: 28468122 bytes'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items:
2472977, Lv2 items: 14953'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 139 - Memory of
derived class: 27766622, Memory for Lv1+Lv2: 10011532'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 165 - Preparing
partitions and calculating bucket sizes... Done. Time elapsed: 0.3913'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 172 - Start main
loop...'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 0 to 3220'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.2495'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.3390'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 3220 to 8274'
2024-12-08 20:40:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.2019'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.3629'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 8274 to 14398'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1868'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.3929'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 14398 to 21590'
2024-12-08 20:40:19 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1810'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.2630'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 21590 to 30086'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1888'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.3353'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 30086 to 40362'
2024-12-08 20:40:20 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1947'
2024-12-08 20:40:21 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.3545'
2024-12-08 20:40:21 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 40362 to 53929'
2024-12-08 20:40:21 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.2144'
2024-12-08 20:40:21 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.4000'
2024-12-08 20:40:21 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 53929 to 65536'
2024-12-08 20:40:22 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1539'
2024-12-08 20:40:22 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1880'
2024-12-08 20:40:22 - b'INFO sorting/base_engine.cpp : 204 - Main loop
done. Time elapsed: 4.2075'
2024-12-08 20:40:22 - b'INFO sorting/base_engine.cpp : 207 -
Postprocessing...'
2024-12-08 20:40:22 - b'INFO sorting/seq_to_sdbg.cpp : 793 - Number of $ A
C G T A- C- G- T-:'
2024-12-08 20:40:22 - b'INFO sorting/seq_to_sdbg.cpp : 794 - 146013 1661295
1514765 1444193 1641565 20069 15354 12710 18497'
2024-12-08 20:40:22 - b'INFO sorting/seq_to_sdbg.cpp : 800 - Total number
of edges: 6474461'
2024-12-08 20:40:22 - b'INFO sorting/seq_to_sdbg.cpp : 801 - Total number
of ONEs: 6261818'
2024-12-08 20:40:22 - b'INFO sorting/seq_to_sdbg.cpp : 802 - Total number
of $v edges: 146013'
2024-12-08 20:40:22 - b'INFO sorting/base_engine.cpp : 210 - Postprocess
done. Time elapsed: 0.2522'
2024-12-08 20:40:22 - b'INFO utils/utils.h : 152 - Real: 6.4784\
tuser: 7.5541\tsys: 0.6003\tmaxrss: 303084'
2024-12-08 20:40:22 - Assemble contigs from SdBG for k = 21
2024-12-08 20:40:22 - command /opt/conda/bin/megahit_core assemble -s
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k21/21 -o
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21 -t 6 --min_standalone 200
--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
2024-12-08 20:40:22 - b'INFO main_assemble.cpp : 129 - Loading
succinct de Bruijn graph:
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k21/21Done. Time elapsed: 0.340073'
2024-12-08 20:40:22 - b'INFO main_assemble.cpp : 133 - Number of
Edges: 6474461; K value: 21'
2024-12-08 20:40:22 - b'INFO main_assemble.cpp : 140 - Number of CPU
threads: 6'
2024-12-08 20:40:24 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 2; Accumulated tips removed: 18762; time elapsed: 0.2620'
2024-12-08 20:40:24 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 4; Accumulated tips removed: 44004; time elapsed: 0.4568'
2024-12-08 20:40:25 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 8; Accumulated tips removed: 70428; time elapsed: 0.7401'
2024-12-08 20:40:26 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 16; Accumulated tips removed: 99610; time elapsed: 1.2374'
2024-12-08 20:40:27 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 32; Accumulated tips removed: 148333; time elapsed: 1.2809'
2024-12-08 20:40:28 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips
with length less than 42; Accumulated tips removed: 155778; time elapsed: 1.0216'
2024-12-08 20:40:28 - b'INFO main_assemble.cpp : 158 - Tips removal
done! Time elapsed(sec): 5.982'
2024-12-08 20:40:32 - b'INFO assembly/unitig_graph.cpp : 83 - Graph size
without loops: 47957, palindrome: 7'
2024-12-08 20:40:32 - b'INFO main_assemble.cpp : 166 - unitig graph
size: 47963, time for building: 3.476'
2024-12-08 20:40:32 - b'INFO assembly/contig_stat.h : 40 - Max: 2150,
Min: 22, N50: 100, number contigs: 47963, number isolated: 10662, number looped: 6,
total size: 3154171,'
2024-12-08 20:40:32 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 1'
2024-12-08 20:40:32 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 470, Time elapsed(sec): 0.213'
2024-12-08 20:40:32 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 53, Time elapsed(sec): 0.193531'
2024-12-08 20:40:33 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 20958, time: 0.193'
2024-12-08 20:40:33 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 121, time: 0.114'
2024-12-08 20:40:33 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 2'
2024-12-08 20:40:33 - b'INFO main_assemble.cpp : 192 - Tips removed:
11988, time: 0.700'
2024-12-08 20:40:33 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 27, Time elapsed(sec): 0.100'
2024-12-08 20:40:34 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 20, Time elapsed(sec): 0.129349'
2024-12-08 20:40:34 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 53, time: 0.123'
2024-12-08 20:40:34 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 9, time: 0.104'
2024-12-08 20:40:34 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 3'
2024-12-08 20:40:34 - b'INFO main_assemble.cpp : 192 - Tips removed:
28, time: 0.579'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.125'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.135512'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 9, time: 0.134'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.018'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 4'
2024-12-08 20:40:35 - b'INFO main_assemble.cpp : 192 - Tips removed:
4, time: 0.604'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.157'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.164764'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 3, time: 0.111'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.024'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 5'
2024-12-08 20:40:36 - b'INFO main_assemble.cpp : 192 - Tips removed:
1, time: 0.539'
2024-12-08 20:40:37 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.100'
2024-12-08 20:40:37 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.126459'
2024-12-08 20:40:37 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.103'
2024-12-08 20:40:37 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.013'
2024-12-08 20:40:37 - b'INFO assembly/contig_stat.h : 40 - Max: 6093,
Min: 22, N50: 179, number contigs: 22108, number isolated: 10997, number looped: 2,
total size: 2414536,'
2024-12-08 20:40:38 - b'INFO main_assemble.cpp : 267 - Time to
output: 1.266749'
2024-12-08 20:40:43 - b'INFO main_assemble.cpp : 286 - Number of
local low depth unitigs removed: 1075, complex bubbles removed: 7, time: 4.606075'
2024-12-08 20:40:43 - b'INFO assembly/contig_stat.h : 40 - Max: 6093,
Min: 22, N50: 191, number contigs: 19895, number isolated: 11156, number looped: 2,
total size: 2351464,'
2024-12-08 20:40:44 - b'INFO utils/utils.h : 152 - Real: 21.4683\
tuser: 28.5486\tsys: 0.1250\tmaxrss: 31900'
2024-12-08 20:40:44 - Local assembly for k = 21
2024-12-08 20:40:44 - command /opt/conda/bin/megahit_core local -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.contigs.fa -l
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib -t 6 -o /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k21.local.fa --kmax 29
2024-12-08 20:40:44 - b'INFO localasm/hash_mapper.cpp : 99 - Number of
contigs: 2426, index size: 135447'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper
construction time elapsed: 0.191315'
2024-12-08 20:40:44 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before
reading, sizeof seq_package: 29757156'
2024-12-08 20:40:44 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading,
sizeof seq_package: 29757156'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time
elapsed: 0.311545'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 330 - Insert size
estimation time elapsed: 0.000003'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 218 - Lib 0: total
1546943 reads, aligned 0, added 0 reads to local assembly'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time
elapsed: 0.142155'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number
of reads to do local assembly: 0'
2024-12-08 20:40:44 - b'INFO localasm/local_assemble.cpp : 346 - Local assembly
time elapsed: 0.026117'
2024-12-08 20:40:44 - b'INFO utils/utils.h : 152 - Real: 0.6855\
tuser: 0.7144\tsys: 0.0327\tmaxrss: 41472'
2024-12-08 20:40:44 - Extract iterative edges from k = 21 to 29
2024-12-08 20:40:44 - command /opt/conda/bin/megahit_core iterate -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.contigs.fa -b
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.bubble_seq.fa -t 6 -k 21
-s 8 -o /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-
46d0-8c1d-6dca72eb4d3e/megahit_output/tmp/k29/29 -r
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib.bin
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 190 - Selected kmer
type size for k: 8'
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 174 - Read 11111
contigs'
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 19160'
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 174 - Read 853
contigs'
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 20532'
2024-12-08 20:40:44 - b'INFO main_iterate.cpp : 123 - Selected kmer
type size for next k: 8'
2024-12-08 20:40:47 - b'INFO main_iterate.cpp : 138 - Processed:
1546943, aligned: 82065. Iterative edges: 61015'
2024-12-08 20:40:47 - b'INFO main_iterate.cpp : 142 - Total:
1546943, aligned: 82065. Iterative edges: 61015'
2024-12-08 20:40:47 - b'INFO utils/utils.h : 152 - Real: 2.4726\
tuser: 2.8859\tsys: 0.0907\tmaxrss: 50952'
2024-12-08 20:40:47 - Build graph for k = 29
2024-12-08 20:40:47 - command /opt/conda/bin/megahit_core seq2sdbg --host_mem
29961916416 --mem_flag 1 --output_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k29/29 --num_cpu_threads 6 -k 29 --kmer_from
21 --input_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k29/29 --addi_contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k21.addi.fa --local_contig /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k21.local.fa --contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k21.contigs.fa --bubble /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k21.bubble_seq.fa
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 148 - Preparing
data...'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 369 - Number edges:
61015'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 413 - Bases to
reserve: 2492874, number contigs: 23658, number multiplicity: 84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 421 - Before
reading, sizeof seq_package: 812492, multiplicity vector: 84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 428 - Read 61015
edges.'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 429 - After reading,
sizeof seq_package: 812492/61015/1830450, multiplicity vector: 61015/84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 458 - Read 16959
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.contigs.fa.'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 459 - After reading
contigs, sizeof seq_package: 1435712/77974/4126408, multiplicity vector:
77974/84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 470 - Read 716
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.bubble_seq.fa.'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 471 - After reading
contigs, sizeof seq_package: 1435712/78690/4202730, multiplicity vector:
78690/84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 484 - Read 489
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.addi.fa.'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 485 - After reading
contigs, sizeof seq_package: 1435712/79179/4344456, multiplicity vector:
79179/84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 498 - Read 0 contigs
from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-
46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k21.local.fa.'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 499 - After reading
contigs, sizeof seq_package: 1435712/79179/4344456, multiplicity vector:
79179/84673'
2024-12-08 20:40:47 - b'INFO sorting/seq_to_sdbg.cpp : 506 - Finally,
sizeof seq_package: 1435712/79179/4344456, multiplicity vector: 79179/84673'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 153 - Preparing
data... Done. Time elapsed: 0.1106'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 156 - Preparing
partitions and calculating bucket sizes...'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory
required: 1892246 bytes'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items:
588432, Lv2 items: 9564'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 139 - Memory of
derived class: 1639026, Memory for Lv1+Lv2: 2468496'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 165 - Preparing
partitions and calculating bucket sizes... Done. Time elapsed: 0.2128'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 172 - Start main
loop...'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 0 to 1917'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1043'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1100'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 1917 to 6864'
2024-12-08 20:40:47 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0909'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1290'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 6864 to 13050'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1290'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1240'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 13050 to 20414'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1390'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1599'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 20414 to 29172'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1663'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1244'
2024-12-08 20:40:48 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 29172 to 39868'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1559'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1400'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 39868 to 54232'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1549'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1460'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 54232 to 65536'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.1285'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0684'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 204 - Main loop
done. Time elapsed: 2.0713'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 207 -
Postprocessing...'
2024-12-08 20:40:49 - b'INFO sorting/seq_to_sdbg.cpp : 793 - Number of $ A
C G T A- C- G- T-:'
2024-12-08 20:40:49 - b'INFO sorting/seq_to_sdbg.cpp : 794 - 33174 976314
912565 887923 964212 976 1002 742 702'
2024-12-08 20:40:49 - b'INFO sorting/seq_to_sdbg.cpp : 800 - Total number
of edges: 3777610'
2024-12-08 20:40:49 - b'INFO sorting/seq_to_sdbg.cpp : 801 - Total number
of ONEs: 3741014'
2024-12-08 20:40:49 - b'INFO sorting/seq_to_sdbg.cpp : 802 - Total number
of $v edges: 33174'
2024-12-08 20:40:49 - b'INFO sorting/base_engine.cpp : 210 - Postprocess
done. Time elapsed: 0.2005'
2024-12-08 20:40:49 - b'INFO utils/utils.h : 152 - Real: 2.6000\
tuser: 3.1159\tsys: 0.0771\tmaxrss: 39996'
2024-12-08 20:40:49 - Assemble contigs from SdBG for k = 29
2024-12-08 20:40:49 - command /opt/conda/bin/megahit_core assemble -s
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k29/29 -o
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29 -t 6 --min_standalone 200
--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
2024-12-08 20:40:50 - b'INFO main_assemble.cpp : 129 - Loading
succinct de Bruijn graph:
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k29/29Done. Time elapsed: 0.300501'
2024-12-08 20:40:50 - b'INFO main_assemble.cpp : 133 - Number of
Edges: 3777610; K value: 29'
2024-12-08 20:40:50 - b'INFO main_assemble.cpp : 140 - Number of CPU
threads: 6'
2024-12-08 20:40:50 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 2; Accumulated tips removed: 1148; time elapsed: 0.1029'
2024-12-08 20:40:51 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 4; Accumulated tips removed: 2782; time elapsed: 0.1563'
2024-12-08 20:40:51 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 8; Accumulated tips removed: 5558; time elapsed: 0.2187'
2024-12-08 20:40:51 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 16; Accumulated tips removed: 10114; time elapsed: 0.4346'
2024-12-08 20:40:52 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 32; Accumulated tips removed: 12120; time elapsed: 0.6727'
2024-12-08 20:40:53 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips
with length less than 58; Accumulated tips removed: 22030; time elapsed: 0.8516'
2024-12-08 20:40:53 - b'INFO main_assemble.cpp : 158 - Tips removal
done! Time elapsed(sec): 2.978'
2024-12-08 20:40:55 - b'INFO assembly/unitig_graph.cpp : 83 - Graph size
without loops: 8795, palindrome: 2'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 166 - unitig graph
size: 8801, time for building: 1.866'
2024-12-08 20:40:55 - b'INFO assembly/contig_stat.h : 40 - Max: 6093,
Min: 30, N50: 314, number contigs: 8801, number isolated: 6772, number looped: 6,
total size: 1847304,'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 1'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 73, Time elapsed(sec): 0.139'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 45, Time elapsed(sec): 0.112135'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 1107, time: 0.114'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 39, time: 0.101'
2024-12-08 20:40:55 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 2'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 192 - Tips removed:
454, time: 0.552'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 1, Time elapsed(sec): 0.114'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 3, Time elapsed(sec): 0.106927'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 3, time: 0.127'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.027'
2024-12-08 20:40:56 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 3'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 192 - Tips removed:
2, time: 0.603'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.138'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.134978'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.132'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.030'
2024-12-08 20:40:57 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 4'
2024-12-08 20:40:58 - b'INFO main_assemble.cpp : 192 - Tips removed:
0, time: 0.562'
2024-12-08 20:40:58 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.096'
2024-12-08 20:40:58 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.119371'
2024-12-08 20:40:58 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.111'
2024-12-08 20:40:58 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.021'
2024-12-08 20:40:58 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 30, N50: 338, number contigs: 7424, number isolated: 6936, number looped: 3,
total size: 1798617,'
2024-12-08 20:40:59 - b'INFO main_assemble.cpp : 267 - Time to
output: 0.781698'
2024-12-08 20:41:01 - b'INFO main_assemble.cpp : 286 - Number of
local low depth unitigs removed: 17, complex bubbles removed: 0, time: 2.409841'
2024-12-08 20:41:01 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 30, N50: 340, number contigs: 7386, number isolated: 6940, number looped: 3,
total size: 1796866,'
2024-12-08 20:41:02 - b'INFO utils/utils.h : 152 - Real: 12.4568\
tuser: 15.9773\tsys: 0.0649\tmaxrss: 23964'
2024-12-08 20:41:02 - Local assembly for k = 29
2024-12-08 20:41:02 - command /opt/conda/bin/megahit_core local -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.contigs.fa -l
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib -t 6 -o /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k29.local.fa --kmax 39
2024-12-08 20:41:02 - b'INFO localasm/hash_mapper.cpp : 99 - Number of
contigs: 2359, index size: 140136'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper
construction time elapsed: 0.151742'
2024-12-08 20:41:02 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before
reading, sizeof seq_package: 29757156'
2024-12-08 20:41:02 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading,
sizeof seq_package: 29757156'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time
elapsed: 0.144214'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 330 - Insert size
estimation time elapsed: 0.000002'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 218 - Lib 0: total
1546943 reads, aligned 0, added 0 reads to local assembly'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time
elapsed: 0.177193'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number
of reads to do local assembly: 0'
2024-12-08 20:41:02 - b'INFO localasm/local_assemble.cpp : 346 - Local assembly
time elapsed: 0.031622'
2024-12-08 20:41:02 - b'INFO utils/utils.h : 152 - Real: 0.5213\
tuser: 0.7287\tsys: 0.0365\tmaxrss: 40960'
2024-12-08 20:41:02 - Extract iterative edges from k = 29 to 39
2024-12-08 20:41:02 - command /opt/conda/bin/megahit_core iterate -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.contigs.fa -b
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.bubble_seq.fa -t 6 -k 29
-s 10 -o /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/tmp/k39/39 -r /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/tmp/reads.lib.bin
2024-12-08 20:41:02 - b'INFO main_iterate.cpp : 190 - Selected kmer
type size for k: 8'
2024-12-08 20:41:02 - b'INFO main_iterate.cpp : 174 - Read 488
contigs'
2024-12-08 20:41:02 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 973'
2024-12-08 20:41:02 - b'INFO main_iterate.cpp : 174 - Read 210
contigs'
2024-12-08 20:41:03 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 1314'
2024-12-08 20:41:03 - b'INFO main_iterate.cpp : 123 - Selected kmer
type size for next k: 12'
2024-12-08 20:41:04 - b'INFO main_iterate.cpp : 138 - Processed:
1546943, aligned: 15266. Iterative edges: 4491'
2024-12-08 20:41:04 - b'INFO main_iterate.cpp : 142 - Total:
1546943, aligned: 15266. Iterative edges: 4491'
2024-12-08 20:41:04 - b'INFO utils/utils.h : 152 - Real: 1.8094\
tuser: 1.9338\tsys: 0.0914\tmaxrss: 49468'
2024-12-08 20:41:04 - Build graph for k = 39
2024-12-08 20:41:04 - command /opt/conda/bin/megahit_core seq2sdbg --host_mem
29961916416 --mem_flag 1 --output_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k39/39 --num_cpu_threads 6 -k 39 --kmer_from
29 --input_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k39/39 --addi_contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k29.addi.fa --local_contig /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k29.local.fa --contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k29.contigs.fa --bubble /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k29.bubble_seq.fa
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 148 - Preparing
data...'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 369 - Number edges:
4491'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 413 - Bases to
reserve: 393784, number contigs: 7648, number multiplicity: 12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 421 - Before
reading, sizeof seq_package: 159640, multiplicity vector: 12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 428 - Read 4491
edges.'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 429 - After reading,
sizeof seq_package: 159640/4491/179640, multiplicity vector: 4491/12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 458 - Read 7400
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.contigs.fa.'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 459 - After reading
contigs, sizeof seq_package: 848776/11891/1977428, multiplicity vector:
11891/12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 470 - Read 190
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.bubble_seq.fa.'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 471 - After reading
contigs, sizeof seq_package: 848776/12081/2002704, multiplicity vector:
12081/12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 484 - Read 14
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.addi.fa.'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 485 - After reading
contigs, sizeof seq_package: 848776/12095/2008275, multiplicity vector:
12095/12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 498 - Read 0 contigs
from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-
46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k29.local.fa.'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 499 - After reading
contigs, sizeof seq_package: 848776/12095/2008275, multiplicity vector:
12095/12139'
2024-12-08 20:41:04 - b'INFO sorting/seq_to_sdbg.cpp : 506 - Finally,
sizeof seq_package: 848776/12095/2008275, multiplicity vector: 12095/12139'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 153 - Preparing
data... Done. Time elapsed: 0.0388'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 156 - Preparing
partitions and calculating bucket sizes...'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory
required: 991582 bytes'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items:
416202, Lv2 items: 852'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 139 - Memory of
derived class: 888774, Memory for Lv1+Lv2: 1678440'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 165 - Preparing
partitions and calculating bucket sizes... Done. Time elapsed: 0.1043'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 172 - Start main
loop...'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 0 to 3683'
2024-12-08 20:41:04 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0499'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0860'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 3683 to 8768'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0445'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0800'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 8768 to 14848'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0669'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0698'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 14848 to 21972'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0679'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1010'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 21972 to 30355'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0587'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0760'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 30355 to 40454'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0488'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0718'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 40454 to 53856'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0488'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0799'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 53856 to 65536'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0539'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0460'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 204 - Main loop
done. Time elapsed: 1.0723'
2024-12-08 20:41:05 - b'INFO sorting/base_engine.cpp : 207 -
Postprocessing...'
2024-12-08 20:41:06 - b'INFO sorting/seq_to_sdbg.cpp : 793 - Number of $ A
C G T A- C- G- T-:'
2024-12-08 20:41:06 - b'INFO sorting/seq_to_sdbg.cpp : 794 - 14679 791527
744367 730362 779512 57 40 41 45'
2024-12-08 20:41:06 - b'INFO sorting/seq_to_sdbg.cpp : 800 - Total number
of edges: 3060630'
2024-12-08 20:41:06 - b'INFO sorting/seq_to_sdbg.cpp : 801 - Total number
of ONEs: 3045768'
2024-12-08 20:41:06 - b'INFO sorting/seq_to_sdbg.cpp : 802 - Total number
of $v edges: 14679'
2024-12-08 20:41:06 - b'INFO sorting/base_engine.cpp : 210 - Postprocess
done. Time elapsed: 0.2725'
2024-12-08 20:41:06 - b'INFO utils/utils.h : 152 - Real: 1.4970\
tuser: 2.0086\tsys: 0.0776\tmaxrss: 38664'
2024-12-08 20:41:06 - Assemble contigs from SdBG for k = 39
2024-12-08 20:41:06 - command /opt/conda/bin/megahit_core assemble -s
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k39/39 -o
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39 -t 6 --min_standalone 200
--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
2024-12-08 20:41:06 - b'INFO main_assemble.cpp : 129 - Loading
succinct de Bruijn graph:
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k39/39Done. Time elapsed: 0.255330'
2024-12-08 20:41:06 - b'INFO main_assemble.cpp : 133 - Number of
Edges: 3060630; K value: 39'
2024-12-08 20:41:06 - b'INFO main_assemble.cpp : 140 - Number of CPU
threads: 6'
2024-12-08 20:41:06 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 2; Accumulated tips removed: 32; time elapsed: 0.0714'
2024-12-08 20:41:07 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 4; Accumulated tips removed: 98; time elapsed: 0.0927'
2024-12-08 20:41:07 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 8; Accumulated tips removed: 232; time elapsed: 0.1426'
2024-12-08 20:41:07 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 16; Accumulated tips removed: 280; time elapsed: 0.2150'
2024-12-08 20:41:07 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 32; Accumulated tips removed: 396; time elapsed: 0.4271'
2024-12-08 20:41:08 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 64; Accumulated tips removed: 3648; time elapsed: 0.7855'
2024-12-08 20:41:09 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips
with length less than 78; Accumulated tips removed: 5456; time elapsed: 0.7680'
2024-12-08 20:41:09 - b'INFO main_assemble.cpp : 158 - Tips removal
done! Time elapsed(sec): 2.871'
2024-12-08 20:41:11 - b'INFO assembly/unitig_graph.cpp : 83 - Graph size
without loops: 4779, palindrome: 0'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 166 - unitig graph
size: 4782, time for building: 2.151'
2024-12-08 20:41:11 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 40, N50: 440, number contigs: 4782, number isolated: 4650, number looped: 3,
total size: 1547962,'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 1'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 7, Time elapsed(sec): 0.097'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 8, Time elapsed(sec): 0.128934'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 7, time: 0.132'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.022'
2024-12-08 20:41:11 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 2'
2024-12-08 20:41:12 - b'INFO main_assemble.cpp : 192 - Tips removed:
5, time: 0.675'
2024-12-08 20:41:12 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.115'
2024-12-08 20:41:12 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 1, Time elapsed(sec): 0.116980'
2024-12-08 20:41:12 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.108'
2024-12-08 20:41:13 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.017'
2024-12-08 20:41:13 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 3'
2024-12-08 20:41:13 - b'INFO main_assemble.cpp : 192 - Tips removed:
0, time: 0.763'
2024-12-08 20:41:13 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.143'
2024-12-08 20:41:14 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.141979'
2024-12-08 20:41:14 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.141'
2024-12-08 20:41:14 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.018'
2024-12-08 20:41:14 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 41, N50: 443, number contigs: 4723, number isolated: 4657, number looped: 1,
total size: 1544662,'
2024-12-08 20:41:15 - b'INFO main_assemble.cpp : 267 - Time to
output: 0.791712'
2024-12-08 20:41:16 - b'INFO main_assemble.cpp : 286 - Number of
local low depth unitigs removed: 1, complex bubbles removed: 0, time: 1.163702'
2024-12-08 20:41:16 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 51, N50: 445, number contigs: 4720, number isolated: 4657, number looped: 1,
total size: 1544490,'
2024-12-08 20:41:16 - b'INFO utils/utils.h : 152 - Real: 10.5512\
tuser: 12.9007\tsys: 0.0658\tmaxrss: 22272'
2024-12-08 20:41:16 - Local assembly for k = 39
2024-12-08 20:41:16 - command /opt/conda/bin/megahit_core local -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.contigs.fa -l
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/reads.lib -t 6 -o /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k39.local.fa --kmax 59
2024-12-08 20:41:16 - b'INFO localasm/hash_mapper.cpp : 99 - Number of
contigs: 2358, index size: 141496'
2024-12-08 20:41:16 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper
construction time elapsed: 0.129960'
2024-12-08 20:41:16 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before
reading, sizeof seq_package: 29757156'
2024-12-08 20:41:17 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading,
sizeof seq_package: 29757156'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time
elapsed: 0.186625'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 330 - Insert size
estimation time elapsed: 0.000003'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 218 - Lib 0: total
1546943 reads, aligned 0, added 0 reads to local assembly'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time
elapsed: 0.160243'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number
of reads to do local assembly: 0'
2024-12-08 20:41:17 - b'INFO localasm/local_assemble.cpp : 346 - Local assembly
time elapsed: 0.009765'
2024-12-08 20:41:17 - b'INFO utils/utils.h : 152 - Real: 0.4999\
tuser: 0.6461\tsys: 0.0430\tmaxrss: 41380'
2024-12-08 20:41:17 - Extract iterative edges from k = 39 to 59
2024-12-08 20:41:17 - command /opt/conda/bin/megahit_core iterate -c
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.contigs.fa -b
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.bubble_seq.fa -t 6 -k 39
-s 20 -o /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/tmp/k59/59 -r /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/tmp/reads.lib.bin
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 190 - Selected kmer
type size for k: 12'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 174 - Read 66
contigs'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 132'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 174 - Read 12
contigs'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 176 - Number of
flank kmers: 152'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 123 - Selected kmer
type size for next k: 16'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 138 - Processed:
1546943, aligned: 0. Iterative edges: 0'
2024-12-08 20:41:17 - b'INFO main_iterate.cpp : 142 - Total:
1546943, aligned: 0. Iterative edges: 0'
2024-12-08 20:41:17 - b'INFO utils/utils.h : 152 - Real: 0.3218\
tuser: 0.3545\tsys: 0.0788\tmaxrss: 49652'
2024-12-08 20:41:17 - Build graph for k = 59
2024-12-08 20:41:17 - command /opt/conda/bin/megahit_core seq2sdbg --host_mem
29961916416 --mem_flag 1 --output_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k59/59 --num_cpu_threads 6 -k 59 --kmer_from
39 --input_prefix
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k59/59 --addi_contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k39.addi.fa --local_contig /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k39.local.fa --contig /storage/diepht/vn-phage-
api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k39.contigs.fa --bubble /storage/diepht/vn-
phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-8c1d-6dca72eb4d3e/
megahit_output/intermediate_contigs/k39.bubble_seq.fa
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 148 - Preparing
data...'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 369 - Number edges:
0'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 413 - Bases to
reserve: 132608, number contigs: 4736, number multiplicity: 4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 421 - Before
reading, sizeof seq_package: 71048, multiplicity vector: 4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 428 - Read 0 edges.'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 429 - After reading,
sizeof seq_package: 71048/0/0, multiplicity vector: 0/4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 458 - Read 4719
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.contigs.fa.'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 459 - After reading
contigs, sizeof seq_package: 568328/4719/1544472, multiplicity vector: 4719/4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 470 - Read 10
contigs from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-
bb48-46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.bubble_seq.fa.'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 471 - After reading
contigs, sizeof seq_package: 568328/4729/1547100, multiplicity vector: 4729/4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 484 - Read 1 contigs
from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-
46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.addi.fa.'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 485 - After reading
contigs, sizeof seq_package: 568328/4730/1547216, multiplicity vector: 4730/4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 498 - Read 0 contigs
from /storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-
46d0-8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k39.local.fa.'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 499 - After reading
contigs, sizeof seq_package: 568328/4730/1547216, multiplicity vector: 4730/4736'
2024-12-08 20:41:17 - b'INFO sorting/seq_to_sdbg.cpp : 506 - Finally,
sizeof seq_package: 568328/4730/1547216, multiplicity vector: 4730/4736'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 153 - Preparing
data... Done. Time elapsed: 0.0416'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 156 - Preparing
partitions and calculating bucket sizes...'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory
required: 674612 bytes'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items:
340694, Lv2 items: 696'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 139 - Memory of
derived class: 589912, Memory for Lv1+Lv2: 1376696'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 165 - Preparing
partitions and calculating bucket sizes... Done. Time elapsed: 0.0967'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 172 - Start main
loop...'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 0 to 3663'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0376'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0888'
2024-12-08 20:41:17 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 3663 to 8723'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0346'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0765'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 8723 to 14776'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0290'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1220'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 14776 to 21879'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0437'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1050'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 21879 to 30238'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0513'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1033'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 30238 to 40353'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0476'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.1096'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 40353 to 53861'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0399'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0847'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning
from bucket 53861 to 65536'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning
done. Large diff: 0. Time elapsed: 0.0288'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching &
sorting done. Time elapsed: 0.0508'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 204 - Main loop
done. Time elapsed: 1.0817'
2024-12-08 20:41:18 - b'INFO sorting/base_engine.cpp : 207 -
Postprocessing...'
2024-12-08 20:41:19 - b'INFO sorting/seq_to_sdbg.cpp : 793 - Number of $ A
C G T A- C- G- T-:'
2024-12-08 20:41:19 - b'INFO sorting/seq_to_sdbg.cpp : 794 - 9444 660417
624250 609294 648091 0 0 0 0'
2024-12-08 20:41:19 - b'INFO sorting/seq_to_sdbg.cpp : 800 - Total number
of edges: 2551496'
2024-12-08 20:41:19 - b'INFO sorting/seq_to_sdbg.cpp : 801 - Total number
of ONEs: 2542052'
2024-12-08 20:41:19 - b'INFO sorting/seq_to_sdbg.cpp : 802 - Total number
of $v edges: 9444'
2024-12-08 20:41:19 - b'INFO sorting/base_engine.cpp : 210 - Postprocess
done. Time elapsed: 0.3536'
2024-12-08 20:41:19 - b'INFO utils/utils.h : 152 - Real: 1.5783\
tuser: 1.5382\tsys: 0.0827\tmaxrss: 37940'
2024-12-08 20:41:19 - Assemble contigs from SdBG for k = 59
2024-12-08 20:41:19 - command /opt/conda/bin/megahit_core assemble -s
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k59/59 -o
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/intermediate_contigs/k59 -t 6 --min_standalone 200
--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 --is_final_round
2024-12-08 20:41:19 - b'INFO main_assemble.cpp : 129 - Loading
succinct de Bruijn graph:
/storage/diepht/vn-phage-api/app/data/output/megahit/results_717f6dfc-bb48-46d0-
8c1d-6dca72eb4d3e/megahit_output/tmp/k59/59Done. Time elapsed: 0.302167'
2024-12-08 20:41:19 - b'INFO main_assemble.cpp : 133 - Number of
Edges: 2551496; K value: 59'
2024-12-08 20:41:19 - b'INFO main_assemble.cpp : 140 - Number of CPU
threads: 6'
2024-12-08 20:41:20 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 2; Accumulated tips removed: 0; time elapsed: 0.0490'
2024-12-08 20:41:20 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 4; Accumulated tips removed: 2; time elapsed: 0.0717'
2024-12-08 20:41:20 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 8; Accumulated tips removed: 2; time elapsed: 0.0835'
2024-12-08 20:41:20 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 16; Accumulated tips removed: 2; time elapsed: 0.1790'
2024-12-08 20:41:20 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 32; Accumulated tips removed: 10; time elapsed: 0.3029'
2024-12-08 20:41:21 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips
with length less than 64; Accumulated tips removed: 658; time elapsed: 0.5274'
2024-12-08 20:41:21 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips
with length less than 118; Accumulated tips removed: 4002; time elapsed: 0.6034'
2024-12-08 20:41:21 - b'INFO main_assemble.cpp : 158 - Tips removal
done! Time elapsed(sec): 2.237'
2024-12-08 20:41:23 - b'INFO assembly/unitig_graph.cpp : 83 - Graph size
without loops: 2721, palindrome: 0'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 166 - unitig graph
size: 2722, time for building: 1.222'
2024-12-08 20:41:23 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 177, N50: 572, number contigs: 2722, number isolated: 2722, number looped: 1,
total size: 1262771,'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 184 - Graph cleaning
round 1'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 200 - Number of
bubbles removed: 0, Time elapsed(sec): 0.101'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 210 - Number of
complex bubbles removed: 0, Time elapsed(sec): 0.093672'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 221 - Number unitigs
disconnected: 0, time: 0.111'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 245 - Unitigs
removed in excessive pruning: 0, time: 0.020'
2024-12-08 20:41:23 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 177, N50: 572, number contigs: 2722, number isolated: 2722, number looped: 1,
total size: 1262771,'
2024-12-08 20:41:23 - b'INFO main_assemble.cpp : 286 - Number of
local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.168030'
2024-12-08 20:41:23 - b'INFO assembly/contig_stat.h : 40 - Max: 6636,
Min: 177, N50: 572, number contigs: 2722, number isolated: 2722, number looped: 1,
total size: 1262771,'
2024-12-08 20:41:24 - b'INFO utils/utils.h : 152 - Real: 5.0158\
tuser: 6.3818\tsys: 0.0469\tmaxrss: 22656'
2024-12-08 20:41:24 - Merging to output final contigs
2024-12-08 20:41:24 - 2359 contigs, total 1194966 bp, min 200 bp, max 6636 bp, avg
506 bp, N50 617 bp
2024-12-08 20:41:24 - ALL DONE. Time elapsed: 89.255986 seconds