RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.24ciDr/RM_22992.TueDec51256262023 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: 1701809784 Database = /dev/shm/rModeler.24ciDr/GCA_902459505.2_aGeoSer1.2 - Sequences = 164 - Bases = 3779430017 - N50 = 413748038 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 513817869-550518975 | [ 2 ] 477116764-513817869 | [ ] 440415658-477116763 | [ ] 403714553-440415658 | [ 1 ] 367013447-403714552 | [ ] 330312342-367013447 | [ ] 293611236-330312341 | [ 1 ] 256910131-293611236 | [ 2 ] 220209025-256910130 | [ ] 183507920-220209025 |* [ 3 ] 146806814-183507919 | [ ] 110105709-146806814 |* [ 3 ] 73404603-110105708 | [ 2 ] 36703498-73404603 |* [ 5 ] 2393-36703498 |************************************************** [ 145 ] Storage Throughput = excellent ( 1223.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040786 bp ( 40018600 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:06:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:29 (hh:mm:ss) Elapsed Time Round Time: 00:44:57 (hh:mm:ss) Elapsed Time : 1257 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25666 repeats masked totaling 5874828 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040113 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10039613 bp After Masking: 4009851 bp Masked: 60.06 % -- Input Database Coverage: 10040113 bp out of 3779430017 bp ( 0.27 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:39 (hh:mm:ss) Elapsed Time, 7648 HSPs Collected Number of families returned by RECON: 1587 Round Time: 00:13:53 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77494 repeats masked totaling 17863605 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040593 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30018907 bp After Masking: 11602345 bp Masked: 61.35 % -- Input Database Coverage: 40080706 bp out of 3779430017 bp ( 1.06 % ) Sampling Time: 00:08:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:23:32 (hh:mm:ss) Elapsed Time, 51016 HSPs Collected Number of families returned by RECON: 5406 Round Time: 00:33:52 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:14:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 244969 repeats masked totaling 55072280 bp(s). - TE Masking time 00:05:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90228904 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90006372 bp After Masking: 33392501 bp Masked: 62.90 % -- Input Database Coverage: 130309610 bp out of 3779430017 bp ( 3.45 % ) Sampling Time: 00:25:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:11:40 (hh:mm:ss) Elapsed Time, 310466 HSPs Collected Number of families returned by RECON: 14559 Round Time: 02:53:58 (hh:mm:ss) Elapsed Time : 633 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:43:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 819843 repeats masked totaling 182578684 bp(s). - TE Masking time 00:23:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270500108 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270029798 bp After Masking: 82747974 bp Masked: 69.36 % -- Input Database Coverage: 400809718 bp out of 3779430017 bp ( 10.61 % ) Sampling Time: 01:18:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 14:38:27 (hh:mm:ss) Elapsed Time, 919967 HSPs Collected Number of families returned by RECON: 37358 Round Time: 17:32:02 (hh:mm:ss) Elapsed Time : 1742 families discovered. RepeatScout/RECON discovery complete: 3785 families found Classification Time: 02:10:48 (hh:mm:ss) Elapsed Time Program Time: 24:09:30 (hh:mm:ss) Elapsed Time