RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xW8eAd/RM_405375.WedMay101027222023 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: 1683739641 Database = /dev/shm/rModeler.xW8eAd/GCA_027557775.1_bGalGal4.pri - Sequences = 246 - Bases = 1094281734 - N50 = 113041671 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185837680-199110625 | [ 1 ] 172564736-185837680 | [ ] 159291791-172564735 | [ ] 146018847-159291791 | [ 1 ] 132745903-146018847 | [ ] 119472958-132745902 | [ ] 106200014-119472958 | [ 1 ] 92927069-106200013 | [ ] 79654125-92927069 | [ 2 ] 66381181-79654125 | [ ] 53108236-66381180 | [ 1 ] 39835292-53108236 | [ ] 26562347-39835291 | [ 3 ] 13289403-26562347 |* [ 8 ] 16459-13289403 |************************************************** [ 229 ] Storage Throughput = fair ( 693.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40134749 bp ( 40025314 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:00 (hh:mm:ss) Elapsed Time Round Time: 00:23:35 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3466 repeats masked totaling 879811 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027556 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10025055 bp After Masking: 8562296 bp Masked: 14.59 % -- Input Database Coverage: 10027556 bp out of 1094281734 bp ( 0.92 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:50 (hh:mm:ss) Elapsed Time, 487 HSPs Collected Number of families returned by RECON: 185 Round Time: 00:10:34 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11081 repeats masked totaling 2871255 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30107113 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30000179 bp After Masking: 25222789 bp Masked: 15.92 % -- Input Database Coverage: 40134669 bp out of 1094281734 bp ( 3.67 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:38:18 (hh:mm:ss) Elapsed Time, 31720 HSPs Collected Number of families returned by RECON: 1293 Round Time: 00:45:36 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33193 repeats masked totaling 7988414 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90199057 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 90011197 bp After Masking: 77659595 bp Masked: 13.72 % -- Input Database Coverage: 130333726 bp out of 1094281734 bp ( 11.91 % ) Sampling Time: 00:18:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:02:26 (hh:mm:ss) Elapsed Time, 62344 HSPs Collected Number of families returned by RECON: 8511 Round Time: 04:36:20 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107154 repeats masked totaling 26601188 bp(s). - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270895919 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 270022727 bp After Masking: 227050805 bp Masked: 15.91 % -- Input Database Coverage: 401229645 bp out of 1094281734 bp ( 36.67 % ) Sampling Time: 01:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 32:13:17 (hh:mm:ss) Elapsed Time, 732592 HSPs Collected Number of families returned by RECON: 56409 Round Time: 33:51:35 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatScout/RECON discovery complete: 404 families found Classification Time: 00:29:28 (hh:mm:ss) Elapsed Time Program Time: 40:17:08 (hh:mm:ss) Elapsed Time