RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HrlC3e/RM_2979110.TueJan160122132024 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: 1705396932 Database = /dev/shm/rModeler.HrlC3e/GCF_029582105.1_OMel1.0 - Sequences = 587 - Bases = 1036256795 - N50 = 76629816 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 138501618-148394521 | [ 1 ] 128608716-138501618 | [ ] 118715814-128608716 | [ ] 108822912-118715814 | [ 2 ] 98930010-108822912 | [ ] 89037108-98930010 | [ ] 79144206-89037108 | [ ] 69251303-79144205 | [ 3 ] 59358401-69251303 | [ 1 ] 49465499-59358401 | [ ] 39572597-49465499 | [ ] 29679695-39572597 | [ 2 ] 19786793-29679695 | [ 5 ] 9893891-19786793 | [ 10 ] 989-9893891 |************************************************** [ 563 ] Storage Throughput = good ( 775.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036747 bp ( 40035147 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:52 (hh:mm:ss) Elapsed Time Round Time: 00:20:40 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2500 repeats masked totaling 499348 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033312 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10032812 bp After Masking: 9216527 bp Masked: 8.14 % -- Input Database Coverage: 10033312 bp out of 1036256795 bp ( 0.97 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:07:38 (hh:mm:ss) Elapsed Time, 1076 HSPs Collected Number of families returned by RECON: 303 Round Time: 00:09:16 (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 : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7425 repeats masked totaling 1610320 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003410 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30002310 bp After Masking: 27581889 bp Masked: 8.07 % -- Input Database Coverage: 40036722 bp out of 1036256795 bp ( 3.86 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:48:12 (hh:mm:ss) Elapsed Time, 7956 HSPs Collected Number of families returned by RECON: 2093 Round Time: 00:52:41 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23422 repeats masked totaling 4871118 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035853 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 90030653 bp After Masking: 82562078 bp Masked: 8.30 % -- Input Database Coverage: 130072575 bp out of 1036256795 bp ( 12.55 % ) Sampling Time: 00:09:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 04:25:12 (hh:mm:ss) Elapsed Time, 54150 HSPs Collected Number of families returned by RECON: 13745 Round Time: 04:38:09 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79870 repeats masked totaling 18205597 bp(s). - TE Masking time 00:03:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041680 bp Num Contigs Represented = 229 Non ambiguous bp: Initial: 270028062 bp After Masking: 244199129 bp Masked: 9.57 % -- Input Database Coverage: 400114255 bp out of 1036256795 bp ( 38.61 % ) Sampling Time: 00:30:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23389380 Comparison Time: 34:10:00 (hh:mm:ss) Elapsed Time, 314232 HSPs Collected Number of families returned by RECON: 87740 Round Time: 36:21:31 (hh:mm:ss) Elapsed Time : 279 families discovered. RepeatScout/RECON discovery complete: 492 families found Classification Time: 00:51:28 (hh:mm:ss) Elapsed Time Program Time: 43:13:45 (hh:mm:ss) Elapsed Time