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comparison test-data/megahit.txt @ 27:7591bce96601 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:18:25 +0000
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26:d2aaac19f42f 27:7591bce96601
1 2025-02-13 13:23:44 - MEGAHIT v1.2.9
2 2025-02-13 13:23:44 - Using megahit_core with POPCNT and BMI2 support
3 2025-02-13 13:23:44 - Convert reads to binary library
4 2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core buildlib /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib
5 2025-02-13 13:23:44 - b'INFO sequence/io/sequence_lib.cpp : 75 - Lib 0 (/data/dnb10/galaxy_db/files/c/5/2/dataset_c52c6559-228d-4131-9eec-f5b8d04f08c8.dat): se, 1 reads, 1232 max length'
6 2025-02-13 13:23:44 - b'INFO utils/utils.h : 152 - Real: 0.2031\tuser: 0.0028\tsys: 0.0074\tmaxrss: 14696'
7 2025-02-13 13:23:44 - Start assembly. Number of CPU threads 10
8 2025-02-13 13:23:44 - k list: 21,29,39,59,79,99,119,141
9 2025-02-13 13:23:44 - Memory used: 83886080
10 2025-02-13 13:23:44 - Extract solid (k+1)-mers for k = 21
11 2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core count -k 21 -m 2 --host_mem 83886080 --mem_flag 1 --output_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --num_cpu_threads 10 --read_lib_file /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib
12 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 148 - Preparing data...'
13 2025-02-13 13:23:44 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 324'
14 2025-02-13 13:23:44 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 324'
15 2025-02-13 13:23:44 - b'INFO sorting/kmer_counter.cpp : 76 - 1 reads, 1232 max read length'
16 2025-02-13 13:23:44 - b'INFO sorting/kmer_counter.cpp : 82 - 2 words per substring, 2 words per edge'
17 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 153 - Preparing data... Done. Time elapsed: 0.0209'
18 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 156 - Preparing partitions and calculating bucket sizes...'
19 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory required: 5243336 bytes'
20 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items: 161, Lv2 items: 30'
21 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 139 - Memory of derived class: 5243252, Memory for Lv1+Lv2: 1124'
22 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 165 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 0.0257'
23 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 172 - Start main loop...'
24 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 0 to 120'
25 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0003'
26 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0022'
27 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 120 to 361'
28 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
29 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
30 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 361 to 602'
31 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
32 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
33 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 602 to 843'
34 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
35 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
36 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 843 to 1084'
37 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
38 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
39 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 1084 to 65536'
40 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0027'
41 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0031'
42 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 204 - Main loop done. Time elapsed: 0.0096'
43 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 207 - Postprocessing...'
44 2025-02-13 13:23:44 - b'INFO sorting/kmer_counter.cpp : 405 - Total number of candidate reads: 1 (1)'
45 2025-02-13 13:23:44 - b'INFO sorting/kmer_counter.cpp : 407 - Total number of solid edges: 26'
46 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 210 - Postprocess done. Time elapsed: 0.0595'
47 2025-02-13 13:23:44 - b'INFO utils/utils.h : 152 - Real: 0.1204\tuser: 0.3707\tsys: 0.0656\tmaxrss: 30296'
48 2025-02-13 13:23:44 - Build graph for k = 21
49 2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core seq2sdbg --host_mem 83886080 --mem_flag 1 --output_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --num_cpu_threads 10 -k 21 --kmer_from 0 --input_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --need_mercy
50 2025-02-13 13:23:44 - b'INFO sorting/base_engine.cpp : 148 - Preparing data...'
51 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 369 - Number edges: 26'
52 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 413 - Bases to reserve: 704, number contigs: 0, number multiplicity: 32'
53 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 421 - Before reading, sizeof seq_package: 184, multiplicity vector: 32'
54 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 428 - Read 26 edges.'
55 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 429 - After reading, sizeof seq_package: 184/26/572, multiplicity vector: 26/32'
56 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 440 - Adding mercy edges...'
57 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 191 - Read 1 reads to search for mercy k-mers'
58 2025-02-13 13:23:44 - b'INFO sorting/seq_to_sdbg.cpp : 355 - Number of reads: 1, Number of mercy edges: 529'
59 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 444 - Done. Time elapsed: 0.2585'
60 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 445 - After adding mercy, sizeof seq_package: 5640/555/12210, multiplicity vector: 555/555'
61 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 506 - Finally, sizeof seq_package: 5640/555/12210, multiplicity vector: 555/555'
62 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 153 - Preparing data... Done. Time elapsed: 0.3852'
63 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 156 - Preparing partitions and calculating bucket sizes...'
64 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 80 - Minimum memory required: 7022 bytes'
65 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 138 - Lv1 items: 444, Lv2 items: 90'
66 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 139 - Memory of derived class: 6870, Memory for Lv1+Lv2: 2496'
67 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 165 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 0.0129'
68 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 172 - Start main loop...'
69 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 0 to 167'
70 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
71 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0005'
72 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 167 to 355'
73 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
74 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
75 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 355 to 543'
76 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
77 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
78 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 543 to 731'
79 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
80 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
81 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 731 to 919'
82 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
83 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
84 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 185 - Lv1 scanning from bucket 919 to 65536'
85 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0026'
86 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 198 - Lv1 fetching & sorting done. Time elapsed: 0.0024'
87 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 204 - Main loop done. Time elapsed: 0.0066'
88 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 207 - Postprocessing...'
89 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 793 - Number of $ A C G T A- C- G- T-:'
90 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 794 - 0 253 302 302 253 0 0 0 0'
91 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 800 - Total number of edges: 1110'
92 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 801 - Total number of ONEs: 1110'
93 2025-02-13 13:23:45 - b'INFO sorting/seq_to_sdbg.cpp : 802 - Total number of $v edges: 0'
94 2025-02-13 13:23:45 - b'INFO sorting/base_engine.cpp : 210 - Postprocess done. Time elapsed: 0.1141'
95 2025-02-13 13:23:45 - b'INFO utils/utils.h : 152 - Real: 0.5262\tuser: 0.5163\tsys: 0.3042\tmaxrss: 269456'
96 2025-02-13 13:23:45 - Assemble contigs from SdBG for k = 21
97 2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core assemble -s /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21 -t 10 --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 2.0 --bubble_level 2 --max_tip_len -1 --careful_bubble
98 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 129 - Loading succinct de Bruijn graph: /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21Done. Time elapsed: 0.148410'
99 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 133 - Number of Edges: 1110; K value: 21'
100 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 140 - Number of CPU threads: 10'
101 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 2; Accumulated tips removed: 0; time elapsed: 0.0000'
102 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 4; Accumulated tips removed: 0; time elapsed: 0.0000'
103 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 8; Accumulated tips removed: 0; time elapsed: 0.0000'
104 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 16; Accumulated tips removed: 0; time elapsed: 0.0000'
105 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 160 - Removing tips with length less than 32; Accumulated tips removed: 0; time elapsed: 0.0000'
106 2025-02-13 13:23:45 - b'INFO assembly/sdbg_pruning.cpp : 169 - Removing tips with length less than 42; Accumulated tips removed: 0; time elapsed: 0.0000'
107 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 158 - Tips removal done! Time elapsed(sec): 0.002'
108 2025-02-13 13:23:45 - b'INFO assembly/unitig_graph.cpp : 83 - Graph size without loops: 0, palindrome: 0'
109 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 166 - unitig graph size: 1, time for building: 0.002'
110 2025-02-13 13:23:45 - b'INFO assembly/contig_stat.h : 40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
111 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 184 - Graph cleaning round 1'
112 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 200 - Number of bubbles removed: 0, Time elapsed(sec): 0.000'
113 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 210 - Number of complex bubbles removed: 0, Time elapsed(sec): 0.000024'
114 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 221 - Number unitigs disconnected: 0, time: 0.000'
115 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 245 - Unitigs removed in excessive pruning: 0, time: 0.000'
116 2025-02-13 13:23:45 - b'INFO assembly/contig_stat.h : 40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
117 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 267 - Time to output: 0.000192'
118 2025-02-13 13:23:45 - b'INFO main_assemble.cpp : 286 - Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.000034'
119 2025-02-13 13:23:45 - b'INFO assembly/contig_stat.h : 40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
120 2025-02-13 13:23:45 - b'INFO utils/utils.h : 152 - Real: 0.1675\tuser: 0.2808\tsys: 0.0330\tmaxrss: 22464'
121 2025-02-13 13:23:45 - Local assembly for k = 21
122 2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core local -c /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.contigs.fa -l /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib -t 10 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.local.fa --kmax 29
123 2025-02-13 13:23:45 - b'INFO localasm/hash_mapper.cpp : 99 - Number of contigs: 0, index size: 0'
124 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 315 - Hash mapper construction time elapsed: 0.003884'
125 2025-02-13 13:23:45 - b'INFO sequence/io/sequence_lib.cpp : 115 - Before reading, sizeof seq_package: 324'
126 2025-02-13 13:23:45 - b'INFO sequence/io/sequence_lib.cpp : 117 - After reading, sizeof seq_package: 324'
127 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 324 - Read lib time elapsed: 0.001268'
128 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 330 - Insert size estimation time elapsed: 0.000001'
129 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 218 - Lib 0: total 1 reads, aligned 0, added 0 reads to local assembly'
130 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 338 - Mapping time elapsed: 0.000047'
131 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 232 - Minimum number of reads to do local assembly: 0'
132 2025-02-13 13:23:45 - b'INFO localasm/local_assemble.cpp : 346 - Local assembly time elapsed: 0.004100'
133 2025-02-13 13:23:45 - b'INFO utils/utils.h : 152 - Real: 0.0094\tuser: 0.0553\tsys: 0.0074\tmaxrss: 14696'
134 2025-02-13 13:23:45 - Extract iterative edges from k = 21 to 29
135 2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core iterate -c /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.contigs.fa -b /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.bubble_seq.fa -t 10 -k 21 -s 8 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k29/29 -r /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib.bin
136 2025-02-13 13:23:45 - b'INFO main_iterate.cpp : 190 - Selected kmer type size for k: 8'
137 2025-02-13 13:23:45 - b'INFO main_iterate.cpp : 123 - Selected kmer type size for next k: 8'
138 2025-02-13 13:23:45 - b'INFO main_iterate.cpp : 138 - Processed: 1, aligned: 0. Iterative edges: 0'
139 2025-02-13 13:23:45 - b'INFO main_iterate.cpp : 142 - Total: 1, aligned: 0. Iterative edges: 0'
140 2025-02-13 13:23:45 - b'INFO utils/utils.h : 152 - Real: 0.0136\tuser: 0.0433\tsys: 0.0101\tmaxrss: 14696'
141 2025-02-13 13:23:45 - Merging to output final contigs
142 2025-02-13 13:23:45 - 1 contigs, total 576 bp, min 576 bp, max 576 bp, avg 576 bp, N50 576 bp
143 2025-02-13 13:23:45 - ALL DONE. Time elapsed: 1.490756 seconds