RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Jpppxh/RM_152577.WedJan110118572023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1673428737 Database = /dev/shm/rModeler.Jpppxh/GCF_903995425.1_mOncTor1.1 - Sequences = 2949 - Bases = 2468394440 - N50 = 116819712 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 168721724-180773261 | [ 1 ] 156670187-168721723 | [ 2 ] 144618651-156670187 | [ 1 ] 132567114-144618650 | [ 3 ] 120515578-132567114 | [ ] 108464041-120515577 | [ 3 ] 96412504-108464040 | [ 1 ] 84360968-96412504 | [ 2 ] 72309431-84360967 | [ 3 ] 60257895-72309431 | [ 5 ] 48206358-60257894 | [ 2 ] 36154821-48206357 | [ 1 ] 24103285-36154821 | [ ] 12051748-24103284 | [ ] 212-12051748 |************************************************** [ 2925 ] Storage Throughput = excellent ( 1028.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40501423 bp ( 40020546 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:17 (hh:mm:ss) Elapsed Time Round Time: 00:26:19 (hh:mm:ss) Elapsed Time : 304 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15359 repeats masked totaling 2853326 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10126371 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10005118 bp After Masking: 6940299 bp Masked: 30.63 % -- Input Database Coverage: 10126371 bp out of 2468394440 bp ( 0.41 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:07:03 (hh:mm:ss) Elapsed Time, 5678 HSPs Collected Number of families returned by RECON: 742 Round Time: 00:08:40 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49838 repeats masked totaling 8966413 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30375051 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30015427 bp After Masking: 20430735 bp Masked: 31.93 % -- Input Database Coverage: 40501422 bp out of 2468394440 bp ( 1.64 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303810 Comparison Time: 00:33:32 (hh:mm:ss) Elapsed Time, 22182 HSPs Collected Number of families returned by RECON: 2484 Round Time: 00:39:10 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157072 repeats masked totaling 28402437 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91100546 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 90013297 bp After Masking: 59787108 bp Masked: 33.58 % -- Input Database Coverage: 131601968 bp out of 2468394440 bp ( 5.33 % ) Sampling Time: 00:13:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2753031 Comparison Time: 03:24:20 (hh:mm:ss) Elapsed Time, 107431 HSPs Collected Number of families returned by RECON: 8015 Round Time: 03:41:48 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 525381 repeats masked totaling 92949433 bp(s). - TE Masking time 00:06:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272591253 bp Num Contigs Represented = 399 Non ambiguous bp: Initial: 270006992 bp After Masking: 171545665 bp Masked: 36.47 % -- Input Database Coverage: 404193221 bp out of 2468394440 bp ( 16.37 % ) Sampling Time: 00:43:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24742095 Comparison Time: 23:55:25 (hh:mm:ss) Elapsed Time, 311844 HSPs Collected Number of families returned by RECON: 36292 Round Time: 25:09:55 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatScout/RECON discovery complete: 943 families found Classification Time: 00:34:48 (hh:mm:ss) Elapsed Time Program Time: 30:40:40 (hh:mm:ss) Elapsed Time