RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7iP1E5/RM_3913019.SatMar231445022024 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: 1711230302 Database = /dev/shm/rModeler.7iP1E5/GCA_036417975.1_bAptMan1.hap2 - Sequences = 349 - Bases = 1593539360 - N50 = 90881787 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207955906-222809338 | [ 1 ] 193102474-207955905 | [ ] 178249043-193102474 | [ ] 163395611-178249042 | [ 1 ] 148542179-163395610 | [ ] 133688748-148542179 | [ 1 ] 118835316-133688747 | [ ] 103981884-118835315 | [ ] 89128453-103981884 | [ 2 ] 74275021-89128452 | [ 1 ] 59421589-74275020 | [ ] 44568158-59421589 | [ 2 ] 29714726-44568157 | [ 3 ] 14861294-29714725 |* [ 12 ] 7863-14861294 |************************************************** [ 326 ] Storage Throughput = excellent ( 1390.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019000 bp ( 40018200 non ambiguous ) - Num Contigs Represented = 103 - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:44 (hh:mm:ss) Elapsed Time Round Time: 00:28:55 (hh:mm:ss) Elapsed Time : 145 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1733 repeats masked totaling 1327433 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033966 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10033766 bp After Masking: 8025643 bp Masked: 20.01 % -- Input Database Coverage: 10033966 bp out of 1593539360 bp ( 0.63 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:42 (hh:mm:ss) Elapsed Time, 157762 HSPs Collected Number of families returned by RECON: 345 Round Time: 00:11:32 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6567 repeats masked totaling 4847434 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024955 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30024355 bp After Masking: 23844646 bp Masked: 20.58 % -- Input Database Coverage: 40058921 bp out of 1593539360 bp ( 2.51 % ) Sampling Time: 00:04:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:36:18 (hh:mm:ss) Elapsed Time, 470187 HSPs Collected Number of families returned by RECON: 1613 Round Time: 00:41:52 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20771 repeats masked totaling 14525826 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029335 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 90026735 bp After Masking: 70726154 bp Masked: 21.44 % -- Input Database Coverage: 130088256 bp out of 1593539360 bp ( 8.16 % ) Sampling Time: 00:14:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 04:27:26 (hh:mm:ss) Elapsed Time, 11507140 HSPs Collected Number of families returned by RECON: 7349 Round Time: 05:01:47 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79750 repeats masked totaling 47193045 bp(s). - TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030101 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 270026647 bp After Masking: 208114527 bp Masked: 22.93 % -- Input Database Coverage: 400118357 bp out of 1593539360 bp ( 25.11 % ) Sampling Time: 00:50:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 32:43:40 (hh:mm:ss) Elapsed Time, 94082426 HSPs Collected Number of families returned by RECON: 41988 Round Time: 34:53:25 (hh:mm:ss) Elapsed Time : 324 families discovered. RepeatScout/RECON discovery complete: 593 families found Classification Time: 01:18:45 (hh:mm:ss) Elapsed Time Program Time: 42:36:16 (hh:mm:ss) Elapsed Time