RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.tzUmU5/RM_2096960.FriApr110710402025 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: 1744380639 Database = /data/tmp/rModeler.tzUmU5/GCA_965113295.1_fLeuLeu2.hap1.1 - Sequences = 876 - Bases = 1198377133 - N50 = 45077053 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 79170606-84825578 | [ 1 ] 73515634-79170605 | [ ] 67860662-73515633 | [ 1 ] 62205690-67860661 | [ 1 ] 56550718-62205689 | [ ] 50895746-56550717 | [ 2 ] 45240774-50895745 | [ 3 ] 39585803-45240774 | [ 9 ] 33930831-39585802 | [ 6 ] 28275859-33930830 | [ 2 ] 22620887-28275858 | [ ] 16965915-22620886 | [ ] 11310943-16965914 | [ ] 5655971-11310942 | [ ] 1000-5655971 |************************************************** [ 851 ] Storage Throughput = excellent ( 1240.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033341 bp ( 40025341 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:17 (hh:mm:ss) Elapsed Time Round Time: 00:34:41 (hh:mm:ss) Elapsed Time : 1226 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16188 repeats masked totaling 3718132 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038751 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10035951 bp After Masking: 5716770 bp Masked: 43.04 % -- Input Database Coverage: 10038751 bp out of 1198377133 bp ( 0.84 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:42 (hh:mm:ss) Elapsed Time, 7591 HSPs Collected Number of families returned by RECON: 1684 Round Time: 00:15:15 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49200 repeats masked totaling 11133802 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034510 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30029310 bp After Masking: 17292734 bp Masked: 42.41 % -- Input Database Coverage: 40073261 bp out of 1198377133 bp ( 3.34 % ) Sampling Time: 00:06:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:25:42 (hh:mm:ss) Elapsed Time, 69147 HSPs Collected Number of families returned by RECON: 5615 Round Time: 00:42:48 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153384 repeats masked totaling 34735104 bp(s). - TE Masking time 00:05:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90056843 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 90038343 bp After Masking: 50321056 bp Masked: 44.11 % -- Input Database Coverage: 130130104 bp out of 1198377133 bp ( 10.86 % ) Sampling Time: 00:20:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 02:54:55 (hh:mm:ss) Elapsed Time, 457869 HSPs Collected Number of families returned by RECON: 15631 Round Time: 04:03:05 (hh:mm:ss) Elapsed Time : 687 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 550569 repeats masked totaling 125325409 bp(s). - TE Masking time 00:23:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270083007 bp Num Contigs Represented = 324 Non ambiguous bp: Initial: 270024831 bp After Masking: 130009474 bp Masked: 51.85 % -- Input Database Coverage: 400213111 bp out of 1198377133 bp ( 33.40 % ) Sampling Time: 01:15:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23471526 Comparison Time: 19:21:15 (hh:mm:ss) Elapsed Time, 1270029 HSPs Collected Number of families returned by RECON: 42371 Round Time: 23:44:35 (hh:mm:ss) Elapsed Time : 1774 families discovered. RepeatScout/RECON discovery complete: 3824 families found Classification Time: 02:37:55 (hh:mm:ss) Elapsed Time Program Time: 31:58:19 (hh:mm:ss) Elapsed Time