RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wI2JXT/RM_39611.SatJan70452462023 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: 1673095965 Database = /dev/shm/rModeler.wI2JXT/GCA_009819595.1_bMerNub1.pri - Sequences = 109 - Bases = 1149356202 - N50 = 50894559 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 76056107-81488222 |* [ 2 ] 70623992-76056106 |* [ 2 ] 65191878-70623992 | [ ] 59759763-65191877 |* [ 3 ] 54327648-59759762 | [ ] 48895534-54327648 |* [ 3 ] 43463419-48895533 |* [ 3 ] 38031304-43463418 |* [ 3 ] 32599190-38031304 | [ 1 ] 27167075-32599189 | [ 1 ] 21734960-27167074 | [ 1 ] 16302846-21734960 |* [ 3 ] 10870731-16302845 |* [ 2 ] 5438616-10870730 |***** [ 8 ] 6502-5438616 |************************************************** [ 77 ] Storage Throughput = excellent ( 1241.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40165727 bp ( 40014599 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:20 (hh:mm:ss) Elapsed Time Round Time: 00:26:17 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2694 repeats masked totaling 975568 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10123713 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10014129 bp After Masking: 8997381 bp Masked: 10.15 % -- Input Database Coverage: 10123713 bp out of 1149356202 bp ( 0.88 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:08:04 (hh:mm:ss) Elapsed Time, 1736 HSPs Collected Number of families returned by RECON: 231 Round Time: 00:08:57 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8091 repeats masked totaling 2785216 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041934 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30000390 bp After Masking: 27001939 bp Masked: 9.99 % -- Input Database Coverage: 40165647 bp out of 1149356202 bp ( 3.49 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:40:55 (hh:mm:ss) Elapsed Time, 5785 HSPs Collected Number of families returned by RECON: 1476 Round Time: 00:43:49 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25373 repeats masked totaling 8279569 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90614600 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90020864 bp After Masking: 81251073 bp Masked: 9.74 % -- Input Database Coverage: 130780247 bp out of 1149356202 bp ( 11.38 % ) Sampling Time: 00:07:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 04:20:58 (hh:mm:ss) Elapsed Time, 33093 HSPs Collected Number of families returned by RECON: 10386 Round Time: 04:30:45 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82974 repeats masked totaling 26567046 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271375343 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270020754 bp After Masking: 241703306 bp Masked: 10.49 % -- Input Database Coverage: 402155590 bp out of 1149356202 bp ( 34.99 % ) Sampling Time: 00:22:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 33:45:03 (hh:mm:ss) Elapsed Time, 185536 HSPs Collected Number of families returned by RECON: 71013 Round Time: 35:10:41 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatScout/RECON discovery complete: 353 families found Classification Time: 00:33:05 (hh:mm:ss) Elapsed Time Program Time: 41:33:34 (hh:mm:ss) Elapsed Time