RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ogEm8O/RM_7312.MonJul10948042024 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: 1719852484 Database = /dev/shm/rModeler.ogEm8O/GCA_026230005.1_fGilOrc1.0.hap1 - Sequences = 179 - Bases = 1263410250 - N50 = 50839473 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 70805957-75862728 | [ 1 ] 65749186-70805956 | [ 2 ] 60692416-65749186 | [ 1 ] 55635645-60692415 | [ 2 ] 50578875-55635645 |* [ 4 ] 45522104-50578874 | [ 3 ] 40465334-45522104 |** [ 9 ] 35408563-40465333 | [ 2 ] 30351793-35408563 | [ 1 ] 25295022-30351792 | [ ] 20238252-25295022 | [ ] 15181481-20238251 | [ ] 10124711-15181481 | [ ] 5067940-10124710 | [ ] 11170-5067940 |************************************************** [ 154 ] Storage Throughput = excellent ( 1053.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010223 bp ( 40009398 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:02 (hh:mm:ss) Elapsed Time Round Time: 00:39:49 (hh:mm:ss) Elapsed Time : 1202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15169 repeats masked totaling 3921087 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024545 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10024445 bp After Masking: 5459168 bp Masked: 45.54 % -- Input Database Coverage: 10024545 bp out of 1263410250 bp ( 0.79 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:01 (hh:mm:ss) Elapsed Time, 8518 HSPs Collected Number of families returned by RECON: 1749 Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44978 repeats masked totaling 11892920 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025593 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30024868 bp After Masking: 16042693 bp Masked: 46.57 % -- Input Database Coverage: 40050138 bp out of 1263410250 bp ( 3.17 % ) Sampling Time: 00:07:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:15 (hh:mm:ss) Elapsed Time, 66664 HSPs Collected Number of families returned by RECON: 5343 Round Time: 00:35:08 (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 : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143486 repeats masked totaling 36858421 bp(s). - TE Masking time 00:04:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030940 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90028840 bp After Masking: 46699941 bp Masked: 48.13 % -- Input Database Coverage: 130081078 bp out of 1263410250 bp ( 10.30 % ) Sampling Time: 00:36:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:44:59 (hh:mm:ss) Elapsed Time, 482494 HSPs Collected Number of families returned by RECON: 14768 Round Time: 03:39:07 (hh:mm:ss) Elapsed Time : 762 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:00:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 525841 repeats masked totaling 133499639 bp(s). - TE Masking time 00:23:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017085 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 270009485 bp After Masking: 117458930 bp Masked: 56.50 % -- Input Database Coverage: 400098163 bp out of 1263410250 bp ( 31.67 % ) Sampling Time: 01:31:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 18:17:58 (hh:mm:ss) Elapsed Time, 1176158 HSPs Collected Number of families returned by RECON: 37322 Round Time: 21:10:03 (hh:mm:ss) Elapsed Time : 1624 families discovered. RepeatScout/RECON discovery complete: 3724 families found Classification Time: 02:54:52 (hh:mm:ss) Elapsed Time Program Time: 29:07:00 (hh:mm:ss) Elapsed Time