RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VOhe0S/RM_81426.FriJan131054342023 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: 1673636073 Database = /dev/shm/rModeler.VOhe0S/GCF_901001165.1_fSalTru1.1 - 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 ( 1318.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41022665 bp ( 40004563 non ambiguous ) - Num Contigs Represented = 124 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:55 (hh:mm:ss) Elapsed Time Round Time: 00:26:30 (hh:mm:ss) Elapsed Time : 956 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15792 repeats masked totaling 4381928 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10350434 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 10018382 bp After Masking: 4053769 bp Masked: 59.54 % -- Input Database Coverage: 10350434 bp out of 2371880186 bp ( 0.44 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 4664 HSPs Collected Number of families returned by RECON: 1179 Round Time: 00:10:04 (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 : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45967 repeats masked totaling 12614833 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30713275 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30027225 bp After Masking: 12978444 bp Masked: 56.78 % -- Input Database Coverage: 41063709 bp out of 2371880186 bp ( 1.73 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 00:24:53 (hh:mm:ss) Elapsed Time, 36664 HSPs Collected Number of families returned by RECON: 3608 Round Time: 00:37:34 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144631 repeats masked totaling 39674480 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92898998 bp Num Contigs Represented = 193 Non ambiguous bp: Initial: 90037440 bp After Masking: 37375353 bp Masked: 58.49 % -- Input Database Coverage: 133962707 bp out of 2371880186 bp ( 5.65 % ) Sampling Time: 00:30:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2776546 Comparison Time: 02:07:40 (hh:mm:ss) Elapsed Time, 245993 HSPs Collected Number of families returned by RECON: 10832 Round Time: 02:46:04 (hh:mm:ss) Elapsed Time : 493 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:12:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 484589 repeats masked totaling 129722463 bp(s). - TE Masking time 00:07:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 279533246 bp Num Contigs Represented = 403 Non ambiguous bp: Initial: 270027520 bp After Masking: 100305234 bp Masked: 62.85 % -- Input Database Coverage: 413495953 bp out of 2371880186 bp ( 17.43 % ) Sampling Time: 01:28:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24974778 Comparison Time: 12:32:59 (hh:mm:ss) Elapsed Time, 708408 HSPs Collected Number of families returned by RECON: 35715 Round Time: 14:51:36 (hh:mm:ss) Elapsed Time : 1061 families discovered. RepeatScout/RECON discovery complete: 2611 families found Classification Time: 01:54:23 (hh:mm:ss) Elapsed Time Program Time: 20:46:11 (hh:mm:ss) Elapsed Time