RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qdEm6x/RM_2398.FriJan130921532023 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: 1673630513 Database = /dev/shm/rModeler.qdEm6x/GCF_009873245.2_mBalMus1.pri.v3 - Sequences = 106 - Bases = 2374868943 - N50 = 113414938 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172609120-184938300 |* [ 2 ] 160279941-172609120 | [ 1 ] 147950762-160279941 | [ ] 135621582-147950761 |* [ 2 ] 123292403-135621582 | [ 1 ] 110963224-123292403 |* [ 2 ] 98634044-110963223 |** [ 4 ] 86304865-98634044 |** [ 4 ] 73975686-86304865 |* [ 3 ] 61646506-73975685 | [ ] 49317327-61646506 |* [ 2 ] 36988148-49317327 | [ ] 24658968-36988147 | [ 1 ] 12329789-24658968 | [ ] 610-12329789 |************************************************** [ 84 ] Storage Throughput = excellent ( 1174.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40485385 bp ( 40005336 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:06 (hh:mm:ss) Elapsed Time Round Time: 00:33:04 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9006 repeats masked totaling 2586441 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10240443 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10039192 bp After Masking: 7411501 bp Masked: 26.17 % -- Input Database Coverage: 10240443 bp out of 2374868943 bp ( 0.43 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:56 (hh:mm:ss) Elapsed Time, 9065 HSPs Collected Number of families returned by RECON: 1076 Round Time: 00:09:13 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31905 repeats masked totaling 9177350 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30284943 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30006145 bp After Masking: 20698109 bp Masked: 31.02 % -- Input Database Coverage: 40525386 bp out of 2374868943 bp ( 1.71 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:32:20 (hh:mm:ss) Elapsed Time, 22742 HSPs Collected Number of families returned by RECON: 2520 Round Time: 00:36:59 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104187 repeats masked totaling 30274861 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90774326 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90032844 bp After Masking: 59359571 bp Masked: 34.07 % -- Input Database Coverage: 131299712 bp out of 2374868943 bp ( 5.53 % ) Sampling Time: 00:10:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 03:25:08 (hh:mm:ss) Elapsed Time, 91486 HSPs Collected Number of families returned by RECON: 8902 Round Time: 03:39:52 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 351342 repeats masked totaling 97953441 bp(s). - TE Masking time 00:06:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272429632 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 270020357 bp After Masking: 170834635 bp Masked: 36.73 % -- Input Database Coverage: 403729344 bp out of 2374868943 bp ( 17.00 % ) Sampling Time: 00:31:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 25:37:33 (hh:mm:ss) Elapsed Time, 212778 HSPs Collected Number of families returned by RECON: 37878 Round Time: 26:42:11 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatScout/RECON discovery complete: 818 families found Classification Time: 00:28:46 (hh:mm:ss) Elapsed Time Program Time: 32:10:05 (hh:mm:ss) Elapsed Time