RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0plUL7/RM_17477.FriDec11108332023 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: 1701457707 Database = /dev/shm/rModeler.0plUL7/GCA_030020385.1_rGavGan2.hap1 - Sequences = 298 - Bases = 2339480201 - N50 = 299523158 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 440602280-472073442 | [ 1 ] 409131118-440602279 | [ ] 377659956-409131117 | [ ] 346188795-377659956 | [ ] 314717633-346188794 | [ ] 283246471-314717632 | [ 2 ] 251775309-283246470 | [ 1 ] 220304148-251775309 | [ ] 188832986-220304147 | [ 1 ] 157361824-188832985 | [ ] 125890662-157361823 | [ ] 94419501-125890662 | [ 1 ] 62948339-94419500 | [ 5 ] 31477177-62948338 | [ 3 ] 6016-31477177 |************************************************** [ 284 ] Storage Throughput = excellent ( 1124.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004407 bp ( 40004207 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:05:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:39 (hh:mm:ss) Elapsed Time Round Time: 00:39:58 (hh:mm:ss) Elapsed Time : 537 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11852 repeats masked totaling 2731389 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001626 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001626 bp After Masking: 7010696 bp Masked: 29.90 % -- Input Database Coverage: 10001626 bp out of 2339480201 bp ( 0.43 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:24:35 (hh:mm:ss) Elapsed Time, 14698 HSPs Collected Number of families returned by RECON: 1440 Round Time: 00:28:32 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37851 repeats masked totaling 8631911 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002780 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30002580 bp After Masking: 20745675 bp Masked: 30.85 % -- Input Database Coverage: 40004406 bp out of 2339480201 bp ( 1.71 % ) Sampling Time: 00:07:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:38:48 (hh:mm:ss) Elapsed Time, 62516 HSPs Collected Number of families returned by RECON: 4292 Round Time: 00:48:53 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133761 repeats masked totaling 29882734 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90087861 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90034409 bp After Masking: 58415064 bp Masked: 35.12 % -- Input Database Coverage: 130092267 bp out of 2339480201 bp ( 5.56 % ) Sampling Time: 00:20:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:18:40 (hh:mm:ss) Elapsed Time, 297461 HSPs Collected Number of families returned by RECON: 11953 Round Time: 03:54:27 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:33:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 470154 repeats masked totaling 106867682 bp(s). - TE Masking time 00:12:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270167790 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270026297 bp After Masking: 158423661 bp Masked: 41.33 % -- Input Database Coverage: 400260057 bp out of 2339480201 bp ( 17.11 % ) Sampling Time: 01:09:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 23:21:34 (hh:mm:ss) Elapsed Time, 625821 HSPs Collected Number of families returned by RECON: 37536 Round Time: 25:26:09 (hh:mm:ss) Elapsed Time : 932 families discovered. RepeatScout/RECON discovery complete: 2047 families found Classification Time: 01:26:45 (hh:mm:ss) Elapsed Time Program Time: 32:44:44 (hh:mm:ss) Elapsed Time