RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dnprhg/RM_18919.MonJul12105422024 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: 1719893141 Database = /dev/shm/rModeler.dnprhg/GCA_036971175.1_sNarBan1.hap2 - Sequences = 445 - Bases = 3110263114 - N50 = 371294313 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 462091797-495097020 | [ 1 ] 429086575-462091797 | [ ] 396081353-429086575 | [ ] 363076130-396081352 | [ 2 ] 330070908-363076130 | [ ] 297065686-330070908 | [ 1 ] 264060464-297065686 | [ ] 231055241-264060463 | [ 2 ] 198050019-231055241 | [ 1 ] 165044797-198050019 | [ 1 ] 132039575-165044797 | [ ] 99034352-132039574 | [ 2 ] 66029130-99034352 | [ 4 ] 33023908-66029130 | [ ] 18686-33023908 |************************************************** [ 431 ] Storage Throughput = excellent ( 1225.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028584 bp ( 40024684 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:05:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:00 (hh:mm:ss) Elapsed Time Round Time: 00:41:31 (hh:mm:ss) Elapsed Time : 766 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18215 repeats masked totaling 4682337 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007331 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10006931 bp After Masking: 3848321 bp Masked: 61.54 % -- Input Database Coverage: 10007331 bp out of 3110263114 bp ( 0.32 % ) Sampling Time: 00:08:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:42 (hh:mm:ss) Elapsed Time, 17767 HSPs Collected Number of families returned by RECON: 741 Round Time: 00:14:56 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59545 repeats masked totaling 14983743 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021173 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30017673 bp After Masking: 11493510 bp Masked: 61.71 % -- Input Database Coverage: 40028504 bp out of 3110263114 bp ( 1.29 % ) Sampling Time: 00:19:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:19:24 (hh:mm:ss) Elapsed Time, 36705 HSPs Collected Number of families returned by RECON: 2367 Round Time: 00:40:31 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 185781 repeats masked totaling 46543243 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037694 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90028791 bp After Masking: 31439678 bp Masked: 65.08 % -- Input Database Coverage: 130066198 bp out of 3110263114 bp ( 4.18 % ) Sampling Time: 01:07:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:49:59 (hh:mm:ss) Elapsed Time, 150391 HSPs Collected Number of families returned by RECON: 6085 Round Time: 03:02:28 (hh:mm:ss) Elapsed Time : 278 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:39:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:32:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 594137 repeats masked totaling 149963029 bp(s). - TE Masking time 00:09:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055087 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 270028642 bp After Masking: 82919333 bp Masked: 69.29 % -- Input Database Coverage: 400121285 bp out of 3110263114 bp ( 12.86 % ) Sampling Time: 03:22:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 18:46:42 (hh:mm:ss) Elapsed Time, 373173 HSPs Collected Number of families returned by RECON: 15847 Round Time: 22:41:29 (hh:mm:ss) Elapsed Time : 618 families discovered. RepeatScout/RECON discovery complete: 1765 families found Classification Time: 01:04:07 (hh:mm:ss) Elapsed Time Program Time: 28:25:03 (hh:mm:ss) Elapsed Time