RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.zAi4ma/RM_2226098.ThuApr241046432025 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: 1745516803 Database = /data/tmp/rModeler.zAi4ma/GCA_048628825.1_ASM4862882v1 - Sequences = 457 - Bases = 571276089 - N50 = 24035035 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 28199000-30213143 | [ 3 ] 26184857-28198999 | [ ] 24170714-26184856 | [ 6 ] 22156571-24170713 | [ 7 ] 20142428-22156570 | [ 3 ] 18128285-20142427 | [ 3 ] 16114142-18128284 | [ 1 ] 14100000-16114142 | [ ] 12085857-14099999 | [ 1 ] 10071714-12085856 | [ ] 8057571-10071713 | [ ] 6043428-8057570 | [ ] 4029285-6043427 | [ ] 2015142-4029284 | [ ] 1000-2015142 |************************************************** [ 433 ] Storage Throughput = excellent ( 1340.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039999 bp ( 40032196 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:55 (hh:mm:ss) Elapsed Time Round Time: 00:13:25 (hh:mm:ss) Elapsed Time : 324 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4013 repeats masked totaling 884068 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033202 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10031799 bp After Masking: 8475177 bp Masked: 15.52 % -- Input Database Coverage: 10033202 bp out of 571276089 bp ( 1.76 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:27 (hh:mm:ss) Elapsed Time, 15220 HSPs Collected Number of families returned by RECON: 691 Round Time: 00:04:56 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14898 repeats masked totaling 3442586 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006780 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30000380 bp After Masking: 23933034 bp Masked: 20.22 % -- Input Database Coverage: 40039982 bp out of 571276089 bp ( 7.01 % ) Sampling Time: 00:03:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:16:35 (hh:mm:ss) Elapsed Time, 18291 HSPs Collected Number of families returned by RECON: 2756 Round Time: 00:23:46 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43579 repeats masked totaling 9741947 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049268 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 90035068 bp After Masking: 73070012 bp Masked: 18.84 % -- Input Database Coverage: 130089250 bp out of 571276089 bp ( 22.77 % ) Sampling Time: 00:09:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 01:59:50 (hh:mm:ss) Elapsed Time, 163955 HSPs Collected Number of families returned by RECON: 11670 Round Time: 02:11:52 (hh:mm:ss) Elapsed Time : 251 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162612 repeats masked totaling 35270099 bp(s). - TE Masking time 00:03:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060806 bp Num Contigs Represented = 273 Non ambiguous bp: Initial: 270020706 bp After Masking: 212655899 bp Masked: 21.24 % -- Input Database Coverage: 400150056 bp out of 571276089 bp ( 70.04 % ) Sampling Time: 00:35:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23567545 Comparison Time: 17:11:09 (hh:mm:ss) Elapsed Time, 474360 HSPs Collected Number of families returned by RECON: 54348 Round Time: 18:10:51 (hh:mm:ss) Elapsed Time : 647 families discovered. RepeatScout/RECON discovery complete: 1263 families found Classification Time: 00:48:29 (hh:mm:ss) Elapsed Time Program Time: 21:53:19 (hh:mm:ss) Elapsed Time