RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.rKJZQs/RM_1021652.TueNov190857482024 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: 1732035467 Database = /data/tmp/rModeler.rKJZQs/GCF_037157495.1_bLatDis1.hap1 - Sequences = 367 - Bases = 1241003407 - N50 = 152777856 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 154974149-166042398 | [ 2 ] 143905901-154974149 | [ 1 ] 132837652-143905900 | [ ] 121769404-132837652 | [ 2 ] 110701156-121769404 | [ 1 ] 99632907-110701155 | [ ] 88564659-99632907 | [ 1 ] 77496410-88564658 | [ ] 66428162-77496410 | [ ] 55359914-66428162 | [ ] 44291665-55359913 | [ ] 33223417-44291665 | [ 1 ] 22155168-33223416 | [ 3 ] 11086920-22155168 | [ 6 ] 18672-11086920 |************************************************** [ 350 ] Storage Throughput = good ( 948.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40144974 bp ( 40024774 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:05 (hh:mm:ss) Elapsed Time Round Time: 00:28:45 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2944 repeats masked totaling 939689 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10072160 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10032160 bp After Masking: 8506645 bp Masked: 15.21 % -- Input Database Coverage: 10072160 bp out of 1241003407 bp ( 0.81 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 36581 HSPs Collected Number of families returned by RECON: 193 Round Time: 00:09:05 (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 : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9366 repeats masked totaling 2997399 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30112814 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30032614 bp After Masking: 25432516 bp Masked: 15.32 % -- Input Database Coverage: 40184974 bp out of 1241003407 bp ( 3.24 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:46:34 (hh:mm:ss) Elapsed Time, 196402 HSPs Collected Number of families returned by RECON: 1128 Round Time: 00:52:16 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29127 repeats masked totaling 9071836 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90243426 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90035617 bp After Masking: 76038043 bp Masked: 15.55 % -- Input Database Coverage: 130428400 bp out of 1241003407 bp ( 10.51 % ) Sampling Time: 00:14:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 05:48:02 (hh:mm:ss) Elapsed Time, 3376866 HSPs Collected Number of families returned by RECON: 7526 Round Time: 06:12:59 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100300 repeats masked totaling 32198817 bp(s). - TE Masking time 00:03:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270426622 bp Num Contigs Represented = 174 Non ambiguous bp: Initial: 270011450 bp After Masking: 223763689 bp Masked: 17.13 % -- Input Database Coverage: 400855022 bp out of 1241003407 bp ( 32.30 % ) Sampling Time: 00:48:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 38:18:09 (hh:mm:ss) Elapsed Time, 13864276 HSPs Collected Number of families returned by RECON: 51526 Round Time: 40:12:51 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatScout/RECON discovery complete: 345 families found Classification Time: 00:26:22 (hh:mm:ss) Elapsed Time Program Time: 48:22:18 (hh:mm:ss) Elapsed Time