RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.diFNDO/RM_10533.MonNov272004382023 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: 1701144277 Database = /dev/shm/rModeler.diFNDO/GCA_027917415.1_aGasCar1.hap2 - Sequences = 590 - Bases = 4305890454 - N50 = 524417645 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 613368234-657180180 | [ 2 ] 569556289-613368234 | [ ] 525744344-569556289 | [ ] 481932398-525744343 | [ 2 ] 438120453-481932398 | [ 2 ] 394308508-438120453 | [ ] 350496562-394308507 | [ ] 306684617-350496562 | [ ] 262872672-306684617 | [ 1 ] 219060726-262872671 | [ ] 175248781-219060726 | [ 3 ] 131436836-175248781 | [ 1 ] 87624890-131436835 | [ ] 43812945-87624890 | [ ] 1000-43812945 |************************************************** [ 579 ] Storage Throughput = excellent ( 1218.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002496 bp ( 40000296 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:09:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:02 (hh:mm:ss) Elapsed Time Round Time: 00:44:38 (hh:mm:ss) Elapsed Time : 806 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16335 repeats masked totaling 5015195 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007017 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 10006017 bp After Masking: 3547061 bp Masked: 64.55 % -- Input Database Coverage: 10007017 bp out of 4305890454 bp ( 0.23 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 10868 HSPs Collected Number of families returned by RECON: 1372 Round Time: 00:09:54 (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 : 00:07:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50627 repeats masked totaling 15607383 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035479 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30034279 bp After Masking: 10294232 bp Masked: 65.73 % -- Input Database Coverage: 40042496 bp out of 4305890454 bp ( 0.93 % ) Sampling Time: 00:13:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:45:34 (hh:mm:ss) Elapsed Time, 68325 HSPs Collected Number of families returned by RECON: 4100 Round Time: 01:01:46 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164776 repeats masked totaling 48616899 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029748 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90023148 bp After Masking: 29095396 bp Masked: 67.68 % -- Input Database Coverage: 130072244 bp out of 4305890454 bp ( 3.02 % ) Sampling Time: 00:41:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:02:18 (hh:mm:ss) Elapsed Time, 293133 HSPs Collected Number of families returned by RECON: 10632 Round Time: 02:54:32 (hh:mm:ss) Elapsed Time : 486 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:03:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:47:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 554926 repeats masked totaling 159682961 bp(s). - TE Masking time 00:14:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044916 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270024248 bp After Masking: 73524014 bp Masked: 72.77 % -- Input Database Coverage: 400117160 bp out of 4305890454 bp ( 9.29 % ) Sampling Time: 02:07:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 11:14:35 (hh:mm:ss) Elapsed Time, 733138 HSPs Collected Number of families returned by RECON: 26967 Round Time: 14:14:56 (hh:mm:ss) Elapsed Time : 1181 families discovered. RepeatScout/RECON discovery complete: 2619 families found Classification Time: 01:46:33 (hh:mm:ss) Elapsed Time Program Time: 20:52:19 (hh:mm:ss) Elapsed Time