RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pwlWKA/RM_5673.MonJan152034582024 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: 1705379697 Database = /dev/shm/rModeler.pwlWKA/GCA_963455335.1_mMarMar1.1 - Sequences = 477 - Bases = 2484650161 - N50 = 148918536 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202922478-217416870 | [ 2 ] 188428087-202922478 | [ 2 ] 173933696-188428087 | [ ] 159439304-173933695 | [ 1 ] 144944913-159439304 | [ 2 ] 130450522-144944913 | [ 2 ] 115956130-130450521 | [ 2 ] 101461739-115956130 | [ 1 ] 86967348-101461739 | [ 3 ] 72472956-86967347 | [ ] 57978565-72472956 | [ 3 ] 43484174-57978565 | [ ] 28989782-43484173 | [ 1 ] 14495391-28989782 | [ 1 ] 1000-14495391 |************************************************** [ 457 ] Storage Throughput = excellent ( 1123.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019026 bp ( 40011026 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:58 (hh:mm:ss) Elapsed Time Round Time: 00:33:20 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10393 repeats masked totaling 2405835 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030197 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10028597 bp After Masking: 7577016 bp Masked: 24.45 % -- Input Database Coverage: 10030197 bp out of 2484650161 bp ( 0.40 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:28 (hh:mm:ss) Elapsed Time, 7644 HSPs Collected Number of families returned by RECON: 876 Round Time: 00:22:44 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34981 repeats masked totaling 7683653 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028756 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30022356 bp After Masking: 22082311 bp Masked: 26.45 % -- Input Database Coverage: 40058953 bp out of 2484650161 bp ( 1.61 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:11:40 (hh:mm:ss) Elapsed Time, 29807 HSPs Collected Number of families returned by RECON: 2534 Round Time: 01:17:58 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110292 repeats masked totaling 25237324 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90054624 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90037224 bp After Masking: 64264044 bp Masked: 28.63 % -- Input Database Coverage: 130113577 bp out of 2484650161 bp ( 5.24 % ) Sampling Time: 00:12:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 04:17:38 (hh:mm:ss) Elapsed Time, 114614 HSPs Collected Number of families returned by RECON: 9565 Round Time: 04:36:36 (hh:mm:ss) Elapsed Time : 160 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383637 repeats masked totaling 85650620 bp(s). - TE Masking time 00:08:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270088423 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 270038414 bp After Masking: 182564079 bp Masked: 32.39 % -- Input Database Coverage: 400202000 bp out of 2484650161 bp ( 16.11 % ) Sampling Time: 00:37:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 30:56:07 (hh:mm:ss) Elapsed Time, 416720 HSPs Collected Number of families returned by RECON: 38325 Round Time: 32:10:21 (hh:mm:ss) Elapsed Time : 367 families discovered. RepeatScout/RECON discovery complete: 762 families found Classification Time: 00:35:03 (hh:mm:ss) Elapsed Time Program Time: 39:36:02 (hh:mm:ss) Elapsed Time