RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.UltAms/RM_2956784.SatNov160543292024 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: 1731764609 Database = /scratch/tmp/rModeler.UltAms/GCA_964266715.1_fMicKit1.1 - Sequences = 1581 - Bases = 752333918 - N50 = 26986887 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32304658-34612063 | [ 1 ] 29997254-32304658 | [ 3 ] 27689850-29997254 | [ 6 ] 25382446-27689850 | [ 3 ] 23075042-25382446 | [ 4 ] 20767637-23075041 | [ 4 ] 18460233-20767637 | [ 1 ] 16152829-18460233 | [ 1 ] 13845425-16152829 | [ ] 11538021-13845425 | [ ] 9230616-11538020 | [ 1 ] 6923212-9230616 | [ ] 4615808-6923212 | [ ] 2308404-4615808 | [ 1 ] 1000-2308404 |************************************************** [ 1556 ] Storage Throughput = excellent ( 1572.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034260 bp ( 40028860 non ambiguous ) - Num Contigs Represented = 205 - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:32 (hh:mm:ss) Elapsed Time Round Time: 00:12:00 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6491 repeats masked totaling 1317777 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007619 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 10006419 bp After Masking: 7233356 bp Masked: 27.71 % -- Input Database Coverage: 10007619 bp out of 752333918 bp ( 1.33 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 5024 HSPs Collected Number of families returned by RECON: 1021 Round Time: 00:03:36 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20751 repeats masked totaling 4009107 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026603 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 30022403 bp After Masking: 21551995 bp Masked: 28.21 % -- Input Database Coverage: 40034222 bp out of 752333918 bp ( 5.32 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303810 Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 32001 HSPs Collected Number of families returned by RECON: 3834 Round Time: 00:14:36 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71241 repeats masked totaling 12930322 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031543 bp Num Contigs Represented = 392 Non ambiguous bp: Initial: 90022543 bp After Masking: 63507941 bp Masked: 29.45 % -- Input Database Coverage: 130065765 bp out of 752333918 bp ( 17.29 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2734291 Comparison Time: 01:10:44 (hh:mm:ss) Elapsed Time, 185554 HSPs Collected Number of families returned by RECON: 14655 Round Time: 01:21:21 (hh:mm:ss) Elapsed Time : 344 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 253176 repeats masked totaling 47856739 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270054107 bp Num Contigs Represented = 931 Non ambiguous bp: Initial: 270025307 bp After Masking: 178912198 bp Masked: 33.74 % -- Input Database Coverage: 400119872 bp out of 752333918 bp ( 53.18 % ) Sampling Time: 00:18:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24622653 Comparison Time: 07:57:30 (hh:mm:ss) Elapsed Time, 629542 HSPs Collected Number of families returned by RECON: 56680 Round Time: 08:45:47 (hh:mm:ss) Elapsed Time : 799 families discovered. RepeatScout/RECON discovery complete: 1559 families found Classification Time: 00:43:01 (hh:mm:ss) Elapsed Time Program Time: 11:20:21 (hh:mm:ss) Elapsed Time