RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ik4S5O/RM_745719.FriMay120959112023 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: 1683910750 Database = /dev/shm/rModeler.ik4S5O/GCA_028389875.1_bPtePen1.pri - Sequences = 179 - Bases = 1269000025 - N50 = 130205582 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202475327-216936262 | [ 1 ] 188014392-202475326 | [ ] 173553457-188014391 | [ ] 159092523-173553457 | [ 1 ] 144631588-159092522 | [ ] 130170653-144631587 | [ 1 ] 115709718-130170652 | [ ] 101248784-115709718 | [ ] 86787849-101248783 | [ ] 72326914-86787848 | [ 2 ] 57865979-72326913 | [ 1 ] 43405045-57865979 | [ 1 ] 28944110-43405044 | [ 3 ] 14483175-28944109 |** [ 9 ] 22241-14483175 |************************************************** [ 160 ] Storage Throughput = good ( 862.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40138154 bp ( 40024927 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:05 (hh:mm:ss) Elapsed Time Round Time: 00:23:40 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 862 repeats masked totaling 356124 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035175 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10034975 bp After Masking: 9229644 bp Masked: 8.03 % -- Input Database Coverage: 10035175 bp out of 1269000025 bp ( 0.79 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:49 (hh:mm:ss) Elapsed Time, 1122 HSPs Collected Number of families returned by RECON: 334 Round Time: 00:10:04 (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 : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3139 repeats masked totaling 1440241 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30142899 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30029872 bp After Masking: 26958602 bp Masked: 10.23 % -- Input Database Coverage: 40178074 bp out of 1269000025 bp ( 3.17 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:42:42 (hh:mm:ss) Elapsed Time, 8365 HSPs Collected Number of families returned by RECON: 1727 Round Time: 00:56:54 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12591 repeats masked totaling 4904425 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90141835 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90038972 bp After Masking: 80773154 bp Masked: 10.29 % -- Input Database Coverage: 130319909 bp out of 1269000025 bp ( 10.27 % ) Sampling Time: 00:13:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 04:35:05 (hh:mm:ss) Elapsed Time, 45314 HSPs Collected Number of families returned by RECON: 9653 Round Time: 04:55:20 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46953 repeats masked totaling 17696935 bp(s). - TE Masking time 00:04:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270268279 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 270033743 bp After Masking: 240207367 bp Masked: 11.05 % -- Input Database Coverage: 400588188 bp out of 1269000025 bp ( 31.57 % ) Sampling Time: 00:37:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 36:21:07 (hh:mm:ss) Elapsed Time, 283515 HSPs Collected Number of families returned by RECON: 58811 Round Time: 37:50:19 (hh:mm:ss) Elapsed Time : 227 families discovered. RepeatScout/RECON discovery complete: 358 families found Classification Time: 00:45:33 (hh:mm:ss) Elapsed Time Program Time: 45:01:50 (hh:mm:ss) Elapsed Time