RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Vjmjyx/RM_115169.MonNov270813472023 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: 1701101627 Database = /dev/shm/rModeler.Vjmjyx/GCF_030867095.1_rAllMis1 - Sequences = 195 - Bases = 2346795873 - N50 = 303743212 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 454156521-486595084 | [ 1 ] 421717958-454156520 | [ ] 389279396-421717958 | [ ] 356840833-389279395 | [ ] 324402271-356840833 | [ ] 291963708-324402270 | [ 2 ] 259525146-291963708 | [ ] 227086583-259525145 | [ 1 ] 194648021-227086583 | [ 1 ] 162209458-194648020 | [ ] 129770896-162209458 | [ ] 97332333-129770895 | [ 1 ] 64893771-97332333 |* [ 6 ] 32455208-64893770 |* [ 4 ] 16646-32455208 |************************************************** [ 179 ] Storage Throughput = excellent ( 1221.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40129911 bp ( 40032866 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:05:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:31 (hh:mm:ss) Elapsed Time Round Time: 00:24:21 (hh:mm:ss) Elapsed Time : 573 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 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12755 repeats masked totaling 2800834 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10048040 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10003936 bp After Masking: 7054637 bp Masked: 29.48 % -- Input Database Coverage: 10048040 bp out of 2346795873 bp ( 0.43 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 14085 HSPs Collected Number of families returned by RECON: 1469 Round Time: 00:09:27 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40402 repeats masked totaling 9002483 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30081864 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30028923 bp After Masking: 20607671 bp Masked: 31.37 % -- Input Database Coverage: 40129904 bp out of 2346795873 bp ( 1.71 % ) Sampling Time: 00:06:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:27:37 (hh:mm:ss) Elapsed Time, 74071 HSPs Collected Number of families returned by RECON: 4552 Round Time: 00:36:20 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138136 repeats masked totaling 30769438 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90469045 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90005746 bp After Masking: 58237732 bp Masked: 35.30 % -- Input Database Coverage: 130598949 bp out of 2346795873 bp ( 5.56 % ) Sampling Time: 00:19:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:44:07 (hh:mm:ss) Elapsed Time, 247042 HSPs Collected Number of families returned by RECON: 11974 Round Time: 03:12:21 (hh:mm:ss) Elapsed Time : 403 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:34:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 472624 repeats masked totaling 106822463 bp(s). - TE Masking time 00:09:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272026072 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 270014010 bp After Masking: 160359567 bp Masked: 40.61 % -- Input Database Coverage: 402625021 bp out of 2346795873 bp ( 17.16 % ) Sampling Time: 01:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 19:38:13 (hh:mm:ss) Elapsed Time, 638869 HSPs Collected Number of families returned by RECON: 40202 Round Time: 21:19:05 (hh:mm:ss) Elapsed Time : 932 families discovered. RepeatScout/RECON discovery complete: 2058 families found Classification Time: 01:10:30 (hh:mm:ss) Elapsed Time Program Time: 26:52:04 (hh:mm:ss) Elapsed Time