RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.R4ut3J/RM_2182645.SatNov161543022024 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: 1731800582 Database = /scratch/tmp/rModeler.R4ut3J/GCA_963989345.1_bClaHye2.1 - Sequences = 272 - Bases = 1206104048 - N50 = 121983391 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193789654-207631701 | [ 1 ] 179947607-193789653 | [ ] 166105560-179947606 | [ ] 152263514-166105560 | [ 1 ] 138421467-152263513 | [ ] 124579420-138421466 | [ ] 110737373-124579419 | [ 1 ] 96895327-110737373 | [ ] 83053280-96895326 | [ 1 ] 69211233-83053279 | [ 1 ] 55369186-69211232 | [ 1 ] 41527140-55369186 | [ ] 27685093-41527139 | [ 3 ] 13843046-27685092 |* [ 9 ] 1000-13843046 |************************************************** [ 254 ] Storage Throughput = excellent ( 1498.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020350 bp ( 40014967 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:10 (hh:mm:ss) Elapsed Time Round Time: 00:11:18 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2262 repeats masked totaling 852758 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022892 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10021492 bp After Masking: 8444124 bp Masked: 15.74 % -- Input Database Coverage: 10022892 bp out of 1206104048 bp ( 0.83 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:28 (hh:mm:ss) Elapsed Time, 754 HSPs Collected Number of families returned by RECON: 287 Round Time: 00:05:36 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6377 repeats masked totaling 2246109 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037378 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30033395 bp After Masking: 25951702 bp Masked: 13.59 % -- Input Database Coverage: 40060270 bp out of 1206104048 bp ( 3.32 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:19:27 (hh:mm:ss) Elapsed Time, 14044 HSPs Collected Number of families returned by RECON: 1837 Round Time: 00:25:00 (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 : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19155 repeats masked totaling 6780663 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037744 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90030744 bp After Masking: 78169303 bp Masked: 13.17 % -- Input Database Coverage: 130098014 bp out of 1206104048 bp ( 10.79 % ) Sampling Time: 00:14:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:12:30 (hh:mm:ss) Elapsed Time, 53883 HSPs Collected Number of families returned by RECON: 10962 Round Time: 02:31:35 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68691 repeats masked totaling 23902444 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024414 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 270003814 bp After Masking: 229951558 bp Masked: 14.83 % -- Input Database Coverage: 400122428 bp out of 1206104048 bp ( 33.17 % ) Sampling Time: 00:44:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 17:04:40 (hh:mm:ss) Elapsed Time, 348751 HSPs Collected Number of families returned by RECON: 64985 Round Time: 18:19:02 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatScout/RECON discovery complete: 367 families found Classification Time: 00:15:24 (hh:mm:ss) Elapsed Time Program Time: 21:47:55 (hh:mm:ss) Elapsed Time