RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.rDM1ia/RM_2155549.FriApr110728432025 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: 1744381723 Database = /data/tmp/rModeler.rDM1ia/GCA_964656455.1_mHalGry1.hap1.1 - Sequences = 171 - Bases = 2400078677 - N50 = 187395039 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202117033-216553034 | [ 3 ] 187681032-202117032 | [ 1 ] 173245031-187681031 | [ 2 ] 158809030-173245030 | [ ] 144373029-158809029 | [ 3 ] 129937028-144373028 | [ 2 ] 115501027-129937027 | [ ] 101065026-115501026 | [ 2 ] 86629025-101065025 | [ 2 ] 72193024-86629024 | [ ] 57757023-72193023 | [ 1 ] 43321022-57757022 | [ ] 28885021-43321021 | [ ] 14449020-28885020 | [ ] 13020-14449020 |************************************************** [ 155 ] Storage Throughput = excellent ( 1224.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031720 bp ( 40028320 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:03:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:11 (hh:mm:ss) Elapsed Time Round Time: 00:28:53 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10095 repeats masked totaling 2515890 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002207 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10001207 bp After Masking: 7379806 bp Masked: 26.21 % -- Input Database Coverage: 10002207 bp out of 2400078677 bp ( 0.42 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 6429 HSPs Collected Number of families returned by RECON: 924 Round Time: 00:08:49 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34497 repeats masked totaling 8217139 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029433 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30027033 bp After Masking: 21314651 bp Masked: 29.02 % -- Input Database Coverage: 40031640 bp out of 2400078677 bp ( 1.67 % ) Sampling Time: 00:04:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:38 (hh:mm:ss) Elapsed Time, 22291 HSPs Collected Number of families returned by RECON: 2569 Round Time: 00:37:14 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112952 repeats masked totaling 28359653 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013501 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90005501 bp After Masking: 60775356 bp Masked: 32.48 % -- Input Database Coverage: 130045141 bp out of 2400078677 bp ( 5.42 % ) Sampling Time: 00:12:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:04:31 (hh:mm:ss) Elapsed Time, 65726 HSPs Collected Number of families returned by RECON: 8417 Round Time: 03:36:21 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 397411 repeats masked totaling 90581002 bp(s). - TE Masking time 00:04:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060982 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270035982 bp After Masking: 176944845 bp Masked: 34.47 % -- Input Database Coverage: 400106123 bp out of 2400078677 bp ( 16.67 % ) Sampling Time: 00:38:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 23:02:52 (hh:mm:ss) Elapsed Time, 300917 HSPs Collected Number of families returned by RECON: 39152 Round Time: 24:59:33 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatScout/RECON discovery complete: 803 families found Classification Time: 00:30:38 (hh:mm:ss) Elapsed Time Program Time: 30:21:28 (hh:mm:ss) Elapsed Time