RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wNgM22/RM_96638.MonJan90537582023 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: 1673271477 Database = /dev/shm/rModeler.wNgM22/GCF_015220075.1_bFalRus1.pri - Sequences = 133 - Bases = 1195847496 - N50 = 92439089 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 118461706-126922963 |* [ 3 ] 110000450-118461706 | [ 1 ] 101539194-110000450 | [ ] 93077938-101539194 | [ ] 84616682-93077938 |* [ 3 ] 76155426-84616682 | [ ] 67694170-76155426 | [ 1 ] 59232913-67694169 | [ 1 ] 50771657-59232913 | [ 1 ] 42310401-50771657 | [ ] 33849145-42310401 |* [ 3 ] 25387889-33849145 | [ 2 ] 16926633-25387889 | [ 2 ] 8465377-16926633 | [ ] 4121-8465377 |************************************************** [ 116 ] Storage Throughput = excellent ( 1014.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40129843 bp ( 40037622 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:58 (hh:mm:ss) Elapsed Time Round Time: 00:24:27 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1392 repeats masked totaling 405734 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001042 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000643 bp After Masking: 9554831 bp Masked: 4.46 % -- Input Database Coverage: 10001042 bp out of 1195847496 bp ( 0.84 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:52 (hh:mm:ss) Elapsed Time, 694 HSPs Collected Number of families returned by RECON: 303 Round Time: 00:07:50 (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 : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3951 repeats masked totaling 1106122 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30128799 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30036977 bp After Masking: 28808481 bp Masked: 4.09 % -- Input Database Coverage: 40129841 bp out of 1195847496 bp ( 3.36 % ) Sampling Time: 00:02:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:37:16 (hh:mm:ss) Elapsed Time, 4793 HSPs Collected Number of families returned by RECON: 1558 Round Time: 00:40:40 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15134 repeats masked totaling 4078200 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90306666 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90004478 bp After Masking: 85521795 bp Masked: 4.98 % -- Input Database Coverage: 130436507 bp out of 1195847496 bp ( 10.91 % ) Sampling Time: 00:08:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 04:19:25 (hh:mm:ss) Elapsed Time, 55077 HSPs Collected Number of families returned by RECON: 9693 Round Time: 04:31:02 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55406 repeats masked totaling 15543943 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270960440 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 270010984 bp After Masking: 253367511 bp Masked: 6.16 % -- Input Database Coverage: 401396947 bp out of 1195847496 bp ( 33.57 % ) Sampling Time: 00:22:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 35:45:44 (hh:mm:ss) Elapsed Time, 168493 HSPs Collected Number of families returned by RECON: 65317 Round Time: 37:04:13 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatScout/RECON discovery complete: 311 families found Classification Time: 00:18:59 (hh:mm:ss) Elapsed Time Program Time: 43:07:11 (hh:mm:ss) Elapsed Time