RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Bgy54V/RM_1516848.WedJul31829362024 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: 1720056575 Database = /dev/shm/rModeler.Bgy54V/GCF_900700415.2_Ch_v2.0.2 - Sequences = 1724 - Bases = 786325606 - N50 = 30022480 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30878650-33084258 | [ 7 ] 28673043-30878650 | [ 8 ] 26467435-28673042 | [ 5 ] 24261828-26467435 | [ 3 ] 22056221-24261828 | [ ] 19850613-22056220 | [ 1 ] 17645006-19850613 | [ ] 15439398-17645005 | [ ] 13233791-15439398 | [ 1 ] 11028184-13233791 | [ 1 ] 8822576-11028183 | [ ] 6616969-8822576 | [ ] 4411361-6616968 | [ ] 2205754-4411361 | [ ] 147-2205754 |************************************************** [ 1698 ] Storage Throughput = excellent ( 1326.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40069625 bp ( 40025611 non ambiguous ) - Num Contigs Represented = 160 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:02 (hh:mm:ss) Elapsed Time Round Time: 00:32:13 (hh:mm:ss) Elapsed Time : 604 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6366 repeats masked totaling 1263594 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10047994 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10036815 bp After Masking: 7671087 bp Masked: 23.57 % -- Input Database Coverage: 10047994 bp out of 786325606 bp ( 1.28 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34191 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 4964 HSPs Collected Number of families returned by RECON: 1329 Round Time: 00:09:08 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19705 repeats masked totaling 3956001 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30061636 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 30028801 bp After Masking: 22743268 bp Masked: 24.26 % -- Input Database Coverage: 40109630 bp out of 786325606 bp ( 5.10 % ) Sampling Time: 00:08:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 314028 Comparison Time: 00:32:02 (hh:mm:ss) Elapsed Time, 41764 HSPs Collected Number of families returned by RECON: 5177 Round Time: 00:42:05 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61467 repeats masked totaling 12236243 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90110506 bp Num Contigs Represented = 307 Non ambiguous bp: Initial: 90013908 bp After Masking: 67733652 bp Masked: 24.75 % -- Input Database Coverage: 130220136 bp out of 786325606 bp ( 16.56 % ) Sampling Time: 00:25:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2809635 Comparison Time: 03:37:18 (hh:mm:ss) Elapsed Time, 265513 HSPs Collected Number of families returned by RECON: 17777 Round Time: 04:13:30 (hh:mm:ss) Elapsed Time : 472 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 241658 repeats masked totaling 49527679 bp(s). - TE Masking time 00:14:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270320338 bp Num Contigs Represented = 778 Non ambiguous bp: Initial: 270000405 bp After Masking: 191304770 bp Masked: 29.15 % -- Input Database Coverage: 400540474 bp out of 786325606 bp ( 50.94 % ) Sampling Time: 01:20:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25372126 Comparison Time: 26:21:18 (hh:mm:ss) Elapsed Time, 926192 HSPs Collected Number of families returned by RECON: 63180 Round Time: 29:17:53 (hh:mm:ss) Elapsed Time : 1117 families discovered. RepeatScout/RECON discovery complete: 2288 families found Classification Time: 02:01:33 (hh:mm:ss) Elapsed Time Program Time: 36:56:22 (hh:mm:ss) Elapsed Time