RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DggU8Z/RM_25287.SatJan132359422024 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: 1705219179 Database = /dev/shm/rModeler.DggU8Z/GCA_031878705.1_mTapInd1.hap2 - Sequences = 193 - Bases = 2477445429 - N50 = 133734361 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 160464699-171925268 | [ 1 ] 149004131-160464699 | [ 3 ] 137543563-149004131 | [ 2 ] 126082995-137543563 |* [ 4 ] 114622427-126082995 | [ ] 103161859-114622427 | [ 1 ] 91701291-103161859 | [ 2 ] 80240723-91701291 | [ 2 ] 68780155-80240723 | [ ] 57319587-68780155 | [ 2 ] 45859019-57319587 | [ 3 ] 34398451-45859019 |* [ 4 ] 22937883-34398451 | [ 2 ] 11477315-22937883 | [ ] 16747-11477315 |************************************************** [ 167 ] Storage Throughput = excellent ( 1111.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029533 bp ( 40029333 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:02:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:10 (hh:mm:ss) Elapsed Time Round Time: 00:35:05 (hh:mm:ss) Elapsed Time : 248 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8901 repeats masked totaling 2153678 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002161 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10002161 bp After Masking: 7818401 bp Masked: 21.83 % -- Input Database Coverage: 10002161 bp out of 2477445429 bp ( 0.40 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:11:41 (hh:mm:ss) Elapsed Time, 12946 HSPs Collected Number of families returned by RECON: 1158 Round Time: 00:13:48 (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 : 00:01:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31399 repeats masked totaling 7791125 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027369 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30027169 bp After Masking: 22148840 bp Masked: 26.24 % -- Input Database Coverage: 40029530 bp out of 2477445429 bp ( 1.62 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 01:06:07 (hh:mm:ss) Elapsed Time, 597047 HSPs Collected Number of families returned by RECON: 2787 Round Time: 01:10:27 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110497 repeats masked totaling 26712870 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035915 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90035715 bp After Masking: 62874004 bp Masked: 30.17 % -- Input Database Coverage: 130065445 bp out of 2477445429 bp ( 5.25 % ) Sampling Time: 00:09:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 04:41:48 (hh:mm:ss) Elapsed Time, 3229317 HSPs Collected Number of families returned by RECON: 9195 Round Time: 05:35:21 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 373527 repeats masked totaling 90044202 bp(s). - TE Masking time 00:06:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007415 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 270004615 bp After Masking: 178984882 bp Masked: 33.71 % -- Input Database Coverage: 400072860 bp out of 2477445429 bp ( 16.15 % ) Sampling Time: 00:30:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 32:59:09 (hh:mm:ss) Elapsed Time, 19134629 HSPs Collected Number of families returned by RECON: 39268 Round Time: 34:15:33 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatScout/RECON discovery complete: 931 families found Classification Time: 00:45:34 (hh:mm:ss) Elapsed Time Program Time: 42:35:48 (hh:mm:ss) Elapsed Time