RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fUc1jE/RM_3696597.FriJul181029552025 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: 1752859795 Database = /dev/shm/rModeler.fUc1jE/GCA_045781095.1_rPanTec1.hap1 - Sequences = 629 - Bases = 2165924875 - N50 = 145022339 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 330191101-353775349 | [ 1 ] 306606853-330191100 | [ ] 283022606-306606853 | [ 1 ] 259438358-283022605 | [ ] 235854111-259438358 | [ ] 212269863-235854110 | [ ] 188685616-212269863 | [ 1 ] 165101368-188685615 | [ ] 141517121-165101368 | [ 1 ] 117932873-141517120 | [ 3 ] 94348626-117932873 | [ 2 ] 70764378-94348625 | [ 2 ] 47180131-70764378 | [ ] 23595883-47180130 | [ 6 ] 11636-23595883 |************************************************** [ 612 ] Storage Throughput = excellent ( 1121.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004764 bp ( 40003764 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:13 (hh:mm:ss) Elapsed Time Round Time: 00:28:57 (hh:mm:ss) Elapsed Time : 563 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:52 (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... 13253 repeats masked totaling 2988598 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003023 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10002223 bp After Masking: 6913927 bp Masked: 30.88 % -- Input Database Coverage: 10003023 bp out of 2165924875 bp ( 0.46 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 10536 HSPs Collected Number of families returned by RECON: 1578 Round Time: 00:06:31 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43254 repeats masked totaling 9401343 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001661 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30001461 bp After Masking: 20127013 bp Masked: 32.91 % -- Input Database Coverage: 40004684 bp out of 2165924875 bp ( 1.85 % ) Sampling Time: 00:04:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:57 (hh:mm:ss) Elapsed Time, 60059 HSPs Collected Number of families returned by RECON: 4735 Round Time: 00:31:30 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149258 repeats masked totaling 32476538 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004789 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 90002009 bp After Masking: 56344485 bp Masked: 37.40 % -- Input Database Coverage: 130009473 bp out of 2165924875 bp ( 6.00 % ) Sampling Time: 00:14:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:53:52 (hh:mm:ss) Elapsed Time, 393401 HSPs Collected Number of families returned by RECON: 13551 Round Time: 03:18:50 (hh:mm:ss) Elapsed Time : 450 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 510582 repeats masked totaling 109985649 bp(s). - TE Masking time 00:12:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019377 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 270013577 bp After Masking: 156824009 bp Masked: 41.92 % -- Input Database Coverage: 400028850 bp out of 2165924875 bp ( 18.47 % ) Sampling Time: 00:47:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 21:20:40 (hh:mm:ss) Elapsed Time, 840379 HSPs Collected Number of families returned by RECON: 44802 Round Time: 23:18:24 (hh:mm:ss) Elapsed Time : 1083 families discovered. RepeatScout/RECON discovery complete: 2263 families found Classification Time: 01:34:17 (hh:mm:ss) Elapsed Time Program Time: 29:18:29 (hh:mm:ss) Elapsed Time