RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9AzgNH/RM_19831.FriJan130906022023 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: 1673629561 Database = /dev/shm/rModeler.9AzgNH/GCA_023634085.1_bFalChe1.pri - Sequences = 282 - Bases = 1309366964 - N50 = 96473976 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 119305764-127826306 | [ 3 ] 110785223-119305764 | [ 1 ] 102264682-110785223 | [ ] 93744140-102264681 | [ 1 ] 85223599-93744140 | [ 2 ] 76703058-85223599 | [ ] 68182517-76703058 | [ 1 ] 59661975-68182516 | [ 1 ] 51141434-59661975 | [ 1 ] 42620893-51141434 | [ ] 34100352-42620893 | [ 4 ] 25579810-34100351 | [ ] 17059269-25579810 | [ 3 ] 8538728-17059269 | [ 2 ] 18187-8538728 |************************************************** [ 263 ] Storage Throughput = excellent ( 1024.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40099634 bp ( 40005122 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:02 (hh:mm:ss) Elapsed Time Round Time: 00:33:36 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1403 repeats masked totaling 462377 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10070859 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10030859 bp After Masking: 8811087 bp Masked: 12.16 % -- Input Database Coverage: 10070859 bp out of 1309366964 bp ( 0.77 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:59 (hh:mm:ss) Elapsed Time, 575 HSPs Collected Number of families returned by RECON: 265 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4374 repeats masked totaling 1425197 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30068849 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30014337 bp After Masking: 26321445 bp Masked: 12.30 % -- Input Database Coverage: 40139708 bp out of 1309366964 bp ( 3.07 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:37:59 (hh:mm:ss) Elapsed Time, 4715 HSPs Collected Number of families returned by RECON: 1369 Round Time: 00:42:26 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13337 repeats masked totaling 4112319 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90279301 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 90020925 bp After Masking: 77540287 bp Masked: 13.86 % -- Input Database Coverage: 130419009 bp out of 1309366964 bp ( 9.96 % ) Sampling Time: 00:12:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 04:30:25 (hh:mm:ss) Elapsed Time, 35846 HSPs Collected Number of families returned by RECON: 8141 Round Time: 04:46:35 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51068 repeats masked totaling 15629918 bp(s). - TE Masking time 00:02:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270819845 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 270019143 bp After Masking: 234597970 bp Masked: 13.12 % -- Input Database Coverage: 401238854 bp out of 1309366964 bp ( 30.64 % ) Sampling Time: 00:35:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 37:03:20 (hh:mm:ss) Elapsed Time, 173085 HSPs Collected Number of families returned by RECON: 56393 Round Time: 39:46:31 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatScout/RECON discovery complete: 367 families found Classification Time: 00:37:46 (hh:mm:ss) Elapsed Time Program Time: 46:35:21 (hh:mm:ss) Elapsed Time