RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QGUIBD/RM_332171.SatDec311119352022 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: 1672514373 Database = /dev/shm/rModeler.QGUIBD/GCF_901765095.1_aMicUni1.1 - Sequences = 1081 - Bases = 4685939420 - 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 ( 1341.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40447465 bp ( 40031947 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:07:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:45 (hh:mm:ss) Elapsed Time Round Time: 00:25:22 (hh:mm:ss) Elapsed Time : 998 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 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22231 repeats masked totaling 5553616 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10051204 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000460 bp After Masking: 4296820 bp Masked: 57.03 % -- Input Database Coverage: 10051204 bp out of 4685939420 bp ( 0.21 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:13 (hh:mm:ss) Elapsed Time, 10886 HSPs Collected Number of families returned by RECON: 1650 Round Time: 00:08:26 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66546 repeats masked totaling 16973143 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30396181 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30031407 bp After Masking: 12585326 bp Masked: 58.09 % -- Input Database Coverage: 40447385 bp out of 4685939420 bp ( 0.86 % ) Sampling Time: 00:08:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:19:57 (hh:mm:ss) Elapsed Time, 58131 HSPs Collected Number of families returned by RECON: 5410 Round Time: 00:30:23 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:20:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 211862 repeats masked totaling 53270040 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90888281 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 90001253 bp After Masking: 35339342 bp Masked: 60.73 % -- Input Database Coverage: 131335666 bp out of 4685939420 bp ( 2.80 % ) Sampling Time: 00:25:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 01:35:23 (hh:mm:ss) Elapsed Time, 270775 HSPs Collected Number of families returned by RECON: 15195 Round Time: 02:11:24 (hh:mm:ss) Elapsed Time : 532 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:03:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 708745 repeats masked totaling 177382414 bp(s). - TE Masking time 00:09:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272893423 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 270016177 bp After Masking: 88372181 bp Masked: 67.27 % -- Input Database Coverage: 404229089 bp out of 4685939420 bp ( 8.63 % ) Sampling Time: 01:22:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23519511 Comparison Time: 08:21:21 (hh:mm:ss) Elapsed Time, 834552 HSPs Collected Number of families returned by RECON: 41374 Round Time: 10:32:28 (hh:mm:ss) Elapsed Time : 1460 families discovered. RepeatScout/RECON discovery complete: 3134 families found Classification Time: 01:19:00 (hh:mm:ss) Elapsed Time Program Time: 15:07:03 (hh:mm:ss) Elapsed Time