RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.c465oE/RM_23399.WedDec62231532023 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: 1701930711 Database = /dev/shm/rModeler.c465oE/GCA_949606895.1_fNotRos5.1 - Sequences = 943 - Bases = 1042906029 - N50 = 93745879 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 90898810-97391511 | [ 5 ] 84406109-90898809 | [ 2 ] 77913408-84406108 | [ 2 ] 71420708-77913408 | [ ] 64928007-71420707 | [ 1 ] 58435306-64928006 | [ 1 ] 51942605-58435305 | [ ] 45449905-51942605 | [ ] 38957204-45449904 | [ ] 32464503-38957203 | [ ] 25971802-32464502 | [ ] 19479102-25971802 | [ 1 ] 12986401-19479101 | [ ] 6493700-12986400 | [ ] 1000-6493700 |************************************************** [ 931 ] Storage Throughput = excellent ( 1168.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40062111 bp ( 40031260 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:21 (hh:mm:ss) Elapsed Time Round Time: 00:41:50 (hh:mm:ss) Elapsed Time : 896 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11467 repeats masked totaling 3552315 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021501 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10012301 bp After Masking: 5758300 bp Masked: 42.49 % -- Input Database Coverage: 10021501 bp out of 1042906029 bp ( 0.96 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 5527 HSPs Collected Number of families returned by RECON: 915 Round Time: 00:08:17 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34791 repeats masked totaling 10722903 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040530 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30018879 bp After Masking: 17040610 bp Masked: 43.23 % -- Input Database Coverage: 40062031 bp out of 1042906029 bp ( 3.84 % ) Sampling Time: 00:09:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:26:40 (hh:mm:ss) Elapsed Time, 42618 HSPs Collected Number of families returned by RECON: 3206 Round Time: 00:37:45 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108051 repeats masked totaling 31901671 bp(s). - TE Masking time 00:04:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90095906 bp Num Contigs Represented = 165 Non ambiguous bp: Initial: 90016842 bp After Masking: 50200853 bp Masked: 44.23 % -- Input Database Coverage: 130157937 bp out of 1042906029 bp ( 12.48 % ) Sampling Time: 00:28:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2666895 Comparison Time: 02:49:26 (hh:mm:ss) Elapsed Time, 273362 HSPs Collected Number of families returned by RECON: 9601 Round Time: 03:26:58 (hh:mm:ss) Elapsed Time : 429 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 371926 repeats masked totaling 109580183 bp(s). - TE Masking time 00:17:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270233859 bp Num Contigs Represented = 356 Non ambiguous bp: Initial: 270016699 bp After Masking: 138070003 bp Masked: 48.87 % -- Input Database Coverage: 400391796 bp out of 1042906029 bp ( 38.39 % ) Sampling Time: 01:19:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23863686 Comparison Time: 19:13:22 (hh:mm:ss) Elapsed Time, 740252 HSPs Collected Number of families returned by RECON: 31735 Round Time: 21:19:38 (hh:mm:ss) Elapsed Time : 1112 families discovered. RepeatScout/RECON discovery complete: 2490 families found Classification Time: 02:32:39 (hh:mm:ss) Elapsed Time Program Time: 28:47:07 (hh:mm:ss) Elapsed Time