RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9z9Gm9/RM_1306765.MonJul151108592024 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: 1721066939 Database = /dev/shm/rModeler.9z9Gm9/GCF_025860055.1_RBS_HiC_50CHRs - Sequences = 1746 - Bases = 2186823573 - N50 = 44035943 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 62814368-67301073 | [ 2 ] 58327664-62814368 | [ 1 ] 53840960-58327664 | [ 2 ] 49354256-53840960 | [ 4 ] 44867552-49354256 | [ 10 ] 40380847-44867551 | [ 15 ] 35894143-40380847 | [ 6 ] 31407439-35894143 | [ 4 ] 26920735-31407439 | [ 4 ] 22434031-26920735 | [ 2 ] 17947326-22434030 | [ ] 13460622-17947326 | [ ] 8973918-13460622 | [ ] 4487214-8973918 | [ ] 510-4487214 |************************************************** [ 1696 ] Storage Throughput = excellent ( 1386.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019415 bp ( 40004225 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:52 (hh:mm:ss) Elapsed Time Round Time: 00:25:57 (hh:mm:ss) Elapsed Time : 1148 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19247 repeats masked totaling 4031146 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022568 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10020568 bp After Masking: 5615386 bp Masked: 43.96 % -- Input Database Coverage: 10022568 bp out of 2186823573 bp ( 0.46 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 14167 HSPs Collected Number of families returned by RECON: 2109 Round Time: 00:08:24 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60165 repeats masked totaling 12177582 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036914 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30023724 bp After Masking: 16418476 bp Masked: 45.31 % -- Input Database Coverage: 40059482 bp out of 2186823573 bp ( 1.83 % ) Sampling Time: 00:05:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:31:30 (hh:mm:ss) Elapsed Time, 89521 HSPs Collected Number of families returned by RECON: 5745 Round Time: 00:41:11 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 197649 repeats masked totaling 40583711 bp(s). - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90078622 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 90036157 bp After Masking: 44994291 bp Masked: 50.03 % -- Input Database Coverage: 130138104 bp out of 2186823573 bp ( 5.95 % ) Sampling Time: 00:16:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2648451 Comparison Time: 02:45:30 (hh:mm:ss) Elapsed Time, 398421 HSPs Collected Number of families returned by RECON: 14583 Round Time: 03:16:20 (hh:mm:ss) Elapsed Time : 702 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 690651 repeats masked totaling 142081116 bp(s). - TE Masking time 00:15:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270126185 bp Num Contigs Represented = 274 Non ambiguous bp: Initial: 270016578 bp After Masking: 115948407 bp Masked: 57.06 % -- Input Database Coverage: 400264289 bp out of 2186823573 bp ( 18.30 % ) Sampling Time: 00:57:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23574411 Comparison Time: 21:58:38 (hh:mm:ss) Elapsed Time, 802680 HSPs Collected Number of families returned by RECON: 39202 Round Time: 24:05:52 (hh:mm:ss) Elapsed Time : 1299 families discovered. RepeatScout/RECON discovery complete: 3392 families found Classification Time: 02:02:43 (hh:mm:ss) Elapsed Time Program Time: 30:40:27 (hh:mm:ss) Elapsed Time