RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xF8KC6/RM_22076.SatDec22254202023 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: 1701586459 Database = /dev/shm/rModeler.xF8KC6/GCA_030445055.1_mDasNov1.hap1 - Sequences = 594 - Bases = 3335791168 - N50 = 127761625 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196419940-210449487 | [ 2 ] 182390393-196419939 | [ 1 ] 168360846-182390392 | [ 1 ] 154331299-168360845 | [ 1 ] 140301753-154331299 | [ ] 126272206-140301752 | [ 5 ] 112242659-126272205 | [ 3 ] 98213112-112242658 | [ 3 ] 84183565-98213111 | [ 1 ] 70154019-84183565 | [ 5 ] 56124472-70154018 | [ 4 ] 42094925-56124471 | [ 1 ] 28065378-42094924 | [ 5 ] 14035831-28065377 | [ ] 6285-14035831 |************************************************** [ 562 ] Storage Throughput = excellent ( 1176.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40289667 bp ( 40015686 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:38 (hh:mm:ss) Elapsed Time Round Time: 00:35:21 (hh:mm:ss) Elapsed Time : 330 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13590 repeats masked totaling 4055397 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10067756 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10003142 bp After Masking: 5817184 bp Masked: 41.85 % -- Input Database Coverage: 10067756 bp out of 3335791168 bp ( 0.30 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 10884 HSPs Collected Number of families returned by RECON: 717 Round Time: 00:07:19 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:58 (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... 43896 repeats masked totaling 13497069 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30221831 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30012464 bp After Masking: 16389943 bp Masked: 45.39 % -- Input Database Coverage: 40289587 bp out of 3335791168 bp ( 1.21 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:25:18 (hh:mm:ss) Elapsed Time, 17499 HSPs Collected Number of families returned by RECON: 1988 Round Time: 00:29:43 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136054 repeats masked totaling 40551974 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90645316 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90001440 bp After Masking: 48646701 bp Masked: 45.95 % -- Input Database Coverage: 130934903 bp out of 3335791168 bp ( 3.93 % ) Sampling Time: 00:11:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 02:44:43 (hh:mm:ss) Elapsed Time, 94299 HSPs Collected Number of families returned by RECON: 7241 Round Time: 03:01:40 (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 : 00:17:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 439584 repeats masked totaling 130368623 bp(s). - TE Masking time 00:08:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271625495 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 270004344 bp After Masking: 137432789 bp Masked: 49.10 % -- Input Database Coverage: 402560398 bp out of 3335791168 bp ( 12.07 % ) Sampling Time: 00:36:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23225520 Comparison Time: 20:06:45 (hh:mm:ss) Elapsed Time, 231644 HSPs Collected Number of families returned by RECON: 27001 Round Time: 21:05:53 (hh:mm:ss) Elapsed Time : 429 families discovered. RepeatScout/RECON discovery complete: 987 families found Classification Time: 00:55:20 (hh:mm:ss) Elapsed Time Program Time: 26:15:16 (hh:mm:ss) Elapsed Time