RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.k2n9AG/RM_2658744.ThuFeb131130332025 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: 1739475031 Database = /dev/shm/rModeler.k2n9AG/GCA_036924085.1_xgAriColu1.0.hap1 - Sequences = 401 - Bases = 2294334993 - N50 = 97781720 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 168021300-180022102 | [ 1 ] 156020498-168021299 | [ 1 ] 144019696-156020497 | [ 1 ] 132018894-144019695 | [ 1 ] 120018092-132018893 | [ 1 ] 108017290-120018091 | [ 1 ] 96016488-108017289 | [ 2 ] 84015687-96016488 | [ 4 ] 72014885-84015686 | [ 5 ] 60014083-72014884 | [ 3 ] 48013281-60014082 | [ 2 ] 36012479-48013280 | [ 2 ] 24011677-36012478 | [ 1 ] 12010875-24011676 | [ ] 10074-12010875 |************************************************** [ 376 ] Storage Throughput = excellent ( 1786.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007847 bp ( 40005447 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:55 (hh:mm:ss) Elapsed Time Round Time: 00:11:23 (hh:mm:ss) Elapsed Time : 770 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20630 repeats masked totaling 4962418 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004505 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10003605 bp After Masking: 2909766 bp Masked: 70.91 % -- Input Database Coverage: 10004505 bp out of 2294334993 bp ( 0.44 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:23 (hh:mm:ss) Elapsed Time, 3013 HSPs Collected Number of families returned by RECON: 745 Round Time: 00:04:07 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62922 repeats masked totaling 14906511 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003338 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30001838 bp After Masking: 8653742 bp Masked: 71.16 % -- Input Database Coverage: 40007843 bp out of 2294334993 bp ( 1.74 % ) Sampling Time: 00:05:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:08:39 (hh:mm:ss) Elapsed Time, 25160 HSPs Collected Number of families returned by RECON: 2373 Round Time: 00:14:29 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 197536 repeats masked totaling 46501215 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014017 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90010717 bp After Masking: 24752903 bp Masked: 72.50 % -- Input Database Coverage: 130021860 bp out of 2294334993 bp ( 5.67 % ) Sampling Time: 00:16:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 00:38:53 (hh:mm:ss) Elapsed Time, 113646 HSPs Collected Number of families returned by RECON: 6240 Round Time: 00:57:21 (hh:mm:ss) Elapsed Time : 297 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 645809 repeats masked totaling 148268353 bp(s). - TE Masking time 00:02:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009777 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 270000477 bp After Masking: 64918380 bp Masked: 75.96 % -- Input Database Coverage: 400031637 bp out of 2294334993 bp ( 17.44 % ) Sampling Time: 00:51:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 03:46:58 (hh:mm:ss) Elapsed Time, 307545 HSPs Collected Number of families returned by RECON: 16008 Round Time: 04:44:27 (hh:mm:ss) Elapsed Time : 696 families discovered. RepeatScout/RECON discovery complete: 1853 families found Classification Time: 00:28:20 (hh:mm:ss) Elapsed Time Program Time: 06:40:07 (hh:mm:ss) Elapsed Time