RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.255AoR/RM_78280.SunJan210028242024 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: 1705825703 Database = /dev/shm/rModeler.255AoR/GCA_028885495.2_NHGRI_mGorGor1-v2.0_mat - Sequences = 225 - Bases = 3554709948 - N50 = 154228409 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 232956429-249594942 | [ 1 ] 216317916-232956428 | [ ] 199679403-216317915 | [ 2 ] 183040890-199679402 | [ 2 ] 166402377-183040889 | [ 2 ] 149763864-166402376 |* [ 5 ] 133125351-149763863 | [ 4 ] 116486838-133125350 | [ 1 ] 99848325-116486837 | [ 3 ] 83209812-99848324 | [ 1 ] 66571299-83209811 | [ 1 ] 49932786-66571298 | [ 2 ] 33294273-49932785 | [ ] 16655760-33294272 | [ ] 17248-16655760 |************************************************** [ 201 ] Storage Throughput = excellent ( 1193.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036208 bp ( 40036208 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:16 (hh:mm:ss) Elapsed Time Round Time: 00:35:58 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11366 repeats masked totaling 2670897 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035685 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10035685 bp After Masking: 5616679 bp Masked: 44.03 % -- Input Database Coverage: 10035685 bp out of 3554709948 bp ( 0.28 % ) Sampling Time: 00:07:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 5577 HSPs Collected Number of families returned by RECON: 819 Round Time: 00:13:38 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34368 repeats masked totaling 8387727 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000521 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30000521 bp After Masking: 15841756 bp Masked: 47.20 % -- Input Database Coverage: 40036206 bp out of 3554709948 bp ( 1.13 % ) Sampling Time: 00:20:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:23:38 (hh:mm:ss) Elapsed Time, 22794 HSPs Collected Number of families returned by RECON: 1943 Round Time: 00:44:52 (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 : 00:03:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116834 repeats masked totaling 28141540 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90111344 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90031330 bp After Masking: 45558316 bp Masked: 49.40 % -- Input Database Coverage: 130147550 bp out of 3554709948 bp ( 3.66 % ) Sampling Time: 01:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:11:39 (hh:mm:ss) Elapsed Time, 79093 HSPs Collected Number of families returned by RECON: 6604 Round Time: 03:15:35 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 381299 repeats masked totaling 91945970 bp(s). - TE Masking time 00:04:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270083082 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 270003075 bp After Masking: 129101838 bp Masked: 52.19 % -- Input Database Coverage: 400230632 bp out of 3554709948 bp ( 11.26 % ) Sampling Time: 03:17:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 15:06:29 (hh:mm:ss) Elapsed Time, 241662 HSPs Collected Number of families returned by RECON: 24673 Round Time: 18:37:27 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 811 families found Classification Time: 00:31:43 (hh:mm:ss) Elapsed Time Program Time: 23:59:13 (hh:mm:ss) Elapsed Time