RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.S7m6wC/RM_15592.SunMay140037002023 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: 1684049814 Database = /dev/shm/rModeler.S7m6wC/GCA_901001165.2_fSalTru1.2 - Sequences = 1441 - Bases = 2371880186 - N50 = 52728040 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 91027565-97529106 | [ 2 ] 84526025-91027565 | [ 1 ] 78024485-84526025 | [ 1 ] 71522945-78024485 | [ 3 ] 65021405-71522945 | [ 2 ] 58519865-65021405 | [ 5 ] 52018325-58519865 | [ 4 ] 45516784-52018324 | [ 12 ] 39015244-45516784 | [ 5 ] 32513704-39015244 | [ 2 ] 26012164-32513704 | [ ] 19510624-26012164 | [ 4 ] 13009084-19510624 | [ ] 6507544-13009084 | [ ] 6004-6507544 |************************************************** [ 1400 ] Storage Throughput = excellent ( 1092.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41421300 bp ( 40013650 non ambiguous ) - Num Contigs Represented = 126 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:54 (hh:mm:ss) Elapsed Time Round Time: 00:26:23 (hh:mm:ss) Elapsed Time : 914 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14802 repeats masked totaling 4156133 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10548725 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 10037027 bp After Masking: 4322449 bp Masked: 56.93 % -- Input Database Coverage: 10548725 bp out of 2371880186 bp ( 0.44 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35778 Comparison Time: 00:05:45 (hh:mm:ss) Elapsed Time, 4312 HSPs Collected Number of families returned by RECON: 1165 Round Time: 00:09:09 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44389 repeats masked totaling 13022743 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30912492 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 30016540 bp After Masking: 12842217 bp Masked: 57.22 % -- Input Database Coverage: 41461217 bp out of 2371880186 bp ( 1.75 % ) Sampling Time: 00:08:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 305371 Comparison Time: 00:23:29 (hh:mm:ss) Elapsed Time, 36745 HSPs Collected Number of families returned by RECON: 3679 Round Time: 00:33:27 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139765 repeats masked totaling 38979485 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92754887 bp Num Contigs Represented = 173 Non ambiguous bp: Initial: 90004524 bp After Masking: 37693459 bp Masked: 58.12 % -- Input Database Coverage: 134216104 bp out of 2371880186 bp ( 5.66 % ) Sampling Time: 00:26:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2741311 Comparison Time: 02:14:41 (hh:mm:ss) Elapsed Time, 256503 HSPs Collected Number of families returned by RECON: 10651 Round Time: 02:51:41 (hh:mm:ss) Elapsed Time : 524 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:05:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474909 repeats masked totaling 130295563 bp(s). - TE Masking time 00:12:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 278774602 bp Num Contigs Represented = 415 Non ambiguous bp: Initial: 270011963 bp After Masking: 99854370 bp Masked: 63.02 % -- Input Database Coverage: 412990706 bp out of 2371880186 bp ( 17.41 % ) Sampling Time: 01:26:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24911211 Comparison Time: 14:46:02 (hh:mm:ss) Elapsed Time, 660535 HSPs Collected Number of families returned by RECON: 35337 Round Time: 17:13:17 (hh:mm:ss) Elapsed Time : 1037 families discovered. RepeatScout/RECON discovery complete: 2580 families found Classification Time: 01:45:43 (hh:mm:ss) Elapsed Time Program Time: 22:59:40 (hh:mm:ss) Elapsed Time