RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.xsom30/RM_3960507.SatApr190615582025 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: 1745068555 Database = /data/tmp/rModeler.xsom30/GCF_037038585.1_bPatFas1.hap1 - Sequences = 360 - Bases = 1454324034 - N50 = 81544918 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201612922-216012892 | [ 1 ] 187212952-201612921 | [ ] 172812983-187212952 | [ ] 158413013-172812982 | [ 1 ] 144013044-158413013 | [ ] 129613074-144013043 | [ ] 115213105-129613074 | [ 1 ] 100813135-115213104 | [ ] 86413166-100813135 | [ ] 72013196-86413165 | [ 2 ] 57613227-72013196 | [ 2 ] 43213257-57613226 | [ 3 ] 28813288-43213257 | [ 2 ] 14413318-28813287 |* [ 9 ] 13349-14413318 |************************************************** [ 339 ] Storage Throughput = excellent ( 1487.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40082489 bp ( 40007436 non ambiguous ) - Num Contigs Represented = 112 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:05 (hh:mm:ss) Elapsed Time Round Time: 00:19:05 (hh:mm:ss) Elapsed Time : 148 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2938 repeats masked totaling 1170579 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025512 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10025512 bp After Masking: 7946032 bp Masked: 20.74 % -- Input Database Coverage: 10025512 bp out of 1454324034 bp ( 0.69 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:35 (hh:mm:ss) Elapsed Time, 18222 HSPs Collected Number of families returned by RECON: 220 Round Time: 00:09:17 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9113 repeats masked totaling 3372499 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30096975 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30021922 bp After Masking: 24123156 bp Masked: 19.65 % -- Input Database Coverage: 40122487 bp out of 1454324034 bp ( 2.76 % ) Sampling Time: 00:09:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:21:05 (hh:mm:ss) Elapsed Time, 354873 HSPs Collected Number of families returned by RECON: 1044 Round Time: 00:31:18 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28539 repeats masked totaling 10155350 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90185653 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 90024640 bp After Masking: 72129966 bp Masked: 19.88 % -- Input Database Coverage: 130308140 bp out of 1454324034 bp ( 8.96 % ) Sampling Time: 00:27:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:22:01 (hh:mm:ss) Elapsed Time, 2141383 HSPs Collected Number of families returned by RECON: 5710 Round Time: 02:50:55 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:35:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100863 repeats masked totaling 35251238 bp(s). - TE Masking time 00:02:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270389416 bp Num Contigs Represented = 254 Non ambiguous bp: Initial: 270039033 bp After Masking: 210788033 bp Masked: 21.94 % -- Input Database Coverage: 400697556 bp out of 1454324034 bp ( 27.55 % ) Sampling Time: 01:45:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 15:39:15 (hh:mm:ss) Elapsed Time, 17302679 HSPs Collected Number of families returned by RECON: 36386 Round Time: 17:41:54 (hh:mm:ss) Elapsed Time : 276 families discovered. RepeatScout/RECON discovery complete: 509 families found Classification Time: 00:28:42 (hh:mm:ss) Elapsed Time Program Time: 22:01:11 (hh:mm:ss) Elapsed Time