RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PIYX7X/RM_9510.MonDec41229592023 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: 1701721799 Database = /dev/shm/rModeler.PIYX7X/GCA_031001685.1_rEryReg1.hap3 - Sequences = 3543 - Bases = 2090234102 - N50 = 1500079 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 12169567-13038270 | [ 1 ] 11300864-12169566 | [ ] 10432161-11300863 | [ 1 ] 9563458-10432160 | [ ] 8694755-9563457 | [ 1 ] 7826052-8694754 | [ 1 ] 6957349-7826051 | [ 2 ] 6088646-6957348 | [ 6 ] 5219943-6088645 | [ 17 ] 4351240-5219942 | [ 22 ] 3482537-4351239 | [ 29 ] 2613834-3482536 |* [ 66 ] 1745131-2613833 |** [ 148 ] 876428-1745130 |******* [ 420 ] 7726-876428 |************************************************** [ 2829 ] Storage Throughput = excellent ( 1130.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031772 bp ( 40031772 non ambiguous ) - Num Contigs Represented = 744 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:58 (hh:mm:ss) Elapsed Time Round Time: 00:32:49 (hh:mm:ss) Elapsed Time : 792 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21560 repeats masked totaling 5076490 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007718 bp Num Contigs Represented = 237 Non ambiguous bp: Initial: 10007718 bp After Masking: 4249981 bp Masked: 57.53 % -- Input Database Coverage: 10007718 bp out of 2090234102 bp ( 0.48 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 13324 HSPs Collected Number of families returned by RECON: 718 Round Time: 00:09:26 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66496 repeats masked totaling 15729430 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023974 bp Num Contigs Represented = 591 Non ambiguous bp: Initial: 30023974 bp After Masking: 11986667 bp Masked: 60.08 % -- Input Database Coverage: 40031692 bp out of 2090234102 bp ( 1.92 % ) Sampling Time: 00:08:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 00:23:46 (hh:mm:ss) Elapsed Time, 23316 HSPs Collected Number of families returned by RECON: 2457 Round Time: 00:40:31 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 204274 repeats masked totaling 47773660 bp(s). - TE Masking time 00:05:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006739 bp Num Contigs Represented = 1211 Non ambiguous bp: Initial: 90006739 bp After Masking: 36374505 bp Masked: 59.59 % -- Input Database Coverage: 130038431 bp out of 2090234102 bp ( 6.22 % ) Sampling Time: 00:22:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2671516 Comparison Time: 02:18:06 (hh:mm:ss) Elapsed Time, 179072 HSPs Collected Number of families returned by RECON: 7858 Round Time: 02:47:27 (hh:mm:ss) Elapsed Time : 341 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:06:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 646926 repeats masked totaling 150337737 bp(s). - TE Masking time 00:19:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270000380 bp Num Contigs Represented = 2065 Non ambiguous bp: Initial: 270000380 bp After Masking: 99975098 bp Masked: 62.97 % -- Input Database Coverage: 400038811 bp out of 2090234102 bp ( 19.14 % ) Sampling Time: 01:27:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24279996 Comparison Time: 16:11:34 (hh:mm:ss) Elapsed Time, 545774 HSPs Collected Number of families returned by RECON: 22825 Round Time: 18:17:27 (hh:mm:ss) Elapsed Time : 820 families discovered. RepeatScout/RECON discovery complete: 2020 families found Classification Time: 01:25:20 (hh:mm:ss) Elapsed Time Program Time: 23:53:00 (hh:mm:ss) Elapsed Time