RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZY4yBX/RM_2798044.WedApr231028102025 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: 1745429289 Database = /dev/shm/rModeler.ZY4yBX/GCA_963675345.1_kaTriClin1.1 - Sequences = 192 - Bases = 906935117 - N50 = 38462795 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 57939633-62078107 | [ 1 ] 53801159-57939632 | [ 1 ] 49662685-53801158 | [ ] 45524211-49662684 | [ ] 41385738-45524211 | [ 2 ] 37247264-41385737 |** [ 8 ] 33108790-37247263 |** [ 7 ] 28970316-33108789 |* [ 4 ] 24831842-28970315 | [ ] 20693369-24831842 | [ ] 16554895-20693368 | [ ] 12416421-16554894 | [ ] 8277947-12416420 | [ ] 4139473-8277946 | [ ] 1000-4139473 |************************************************** [ 169 ] Storage Throughput = excellent ( 1677.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017328 bp ( 40010528 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:04:58 (hh:mm:ss) Elapsed Time Round Time: 00:11:08 (hh:mm:ss) Elapsed Time : 841 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13497 repeats masked totaling 4221675 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040650 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10039050 bp After Masking: 5748536 bp Masked: 42.74 % -- Input Database Coverage: 10040650 bp out of 906935117 bp ( 1.11 % ) Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 15615 HSPs Collected Number of families returned by RECON: 1813 Round Time: 00:03:24 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43506 repeats masked totaling 13702789 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016678 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30011478 bp After Masking: 16082175 bp Masked: 46.41 % -- Input Database Coverage: 40057328 bp out of 906935117 bp ( 4.42 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:11:57 (hh:mm:ss) Elapsed Time, 60400 HSPs Collected Number of families returned by RECON: 5713 Round Time: 00:14:22 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138738 repeats masked totaling 42013425 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040973 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90025543 bp After Masking: 47292305 bp Masked: 47.47 % -- Input Database Coverage: 130098301 bp out of 906935117 bp ( 14.34 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:03:53 (hh:mm:ss) Elapsed Time, 371460 HSPs Collected Number of families returned by RECON: 14798 Round Time: 01:20:50 (hh:mm:ss) Elapsed Time : 711 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 510526 repeats masked totaling 152607286 bp(s). - TE Masking time 00:07:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043965 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 270005165 bp After Masking: 115580716 bp Masked: 57.19 % -- Input Database Coverage: 400142266 bp out of 906935117 bp ( 44.12 % ) Sampling Time: 00:13:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 06:02:15 (hh:mm:ss) Elapsed Time, 1144829 HSPs Collected Number of families returned by RECON: 35067 Round Time: 06:44:30 (hh:mm:ss) Elapsed Time : 1902 families discovered. RepeatScout/RECON discovery complete: 3592 families found Classification Time: 01:51:45 (hh:mm:ss) Elapsed Time Program Time: 10:25:59 (hh:mm:ss) Elapsed Time