RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BDBq8B/RM_17850.TueDec51229152023 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: 1701808154 Database = /dev/shm/rModeler.BDBq8B/GCA_901765095.2_aMicUni1.2 - Sequences = 1081 - Bases = 4685939421 - N50 = 535506559 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 721403511-772932187 | [ 1 ] 669874835-721403510 | [ ] 618346159-669874834 | [ 1 ] 566817483-618346158 | [ ] 515288807-566817482 | [ 1 ] 463760131-515288806 | [ ] 412231455-463760130 | [ ] 360702779-412231454 | [ 2 ] 309174103-360702778 | [ 2 ] 257645427-309174102 | [ ] 206116751-257645426 | [ 4 ] 154588075-206116750 | [ ] 103059399-154588074 | [ 2 ] 51530723-103059398 | [ 1 ] 2048-51530723 |************************************************** [ 1067 ] Storage Throughput = excellent ( 1173.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40248286 bp ( 40026287 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:09:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:55 (hh:mm:ss) Elapsed Time Round Time: 00:41:56 (hh:mm:ss) Elapsed Time : 963 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21500 repeats masked totaling 5434302 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10175104 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10039514 bp After Masking: 4418910 bp Masked: 55.98 % -- Input Database Coverage: 10175104 bp out of 4685939421 bp ( 0.22 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 11970 HSPs Collected Number of families returned by RECON: 1713 Round Time: 00:09:20 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:06:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65841 repeats masked totaling 16361257 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30113103 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30026694 bp After Masking: 13161373 bp Masked: 56.17 % -- Input Database Coverage: 40288207 bp out of 4685939421 bp ( 0.86 % ) Sampling Time: 00:09:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:38:06 (hh:mm:ss) Elapsed Time, 74664 HSPs Collected Number of families returned by RECON: 5602 Round Time: 00:50:07 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214303 repeats masked totaling 52773573 bp(s). - TE Masking time 00:04:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90909651 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90015333 bp After Masking: 35829935 bp Masked: 60.20 % -- Input Database Coverage: 131197858 bp out of 4685939421 bp ( 2.80 % ) Sampling Time: 00:28:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 02:21:42 (hh:mm:ss) Elapsed Time, 298814 HSPs Collected Number of families returned by RECON: 15125 Round Time: 03:07:38 (hh:mm:ss) Elapsed Time : 561 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:02:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 718642 repeats masked totaling 177946891 bp(s). - TE Masking time 00:19:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272979862 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 270036076 bp After Masking: 87924667 bp Masked: 67.44 % -- Input Database Coverage: 404177720 bp out of 4685939421 bp ( 8.63 % ) Sampling Time: 01:32:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23464675 Comparison Time: 15:27:29 (hh:mm:ss) Elapsed Time, 781393 HSPs Collected Number of families returned by RECON: 40864 Round Time: 18:32:21 (hh:mm:ss) Elapsed Time : 1447 families discovered. RepeatScout/RECON discovery complete: 3131 families found Classification Time: 01:57:34 (hh:mm:ss) Elapsed Time Program Time: 25:18:56 (hh:mm:ss) Elapsed Time