RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.33fjII/RM_405467.WedMay101028112023 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: 1683739690 Database = /dev/shm/rModeler.33fjII/GCA_027559615.1_bAcrTri1.pri - Sequences = 455 - Bases = 1193419045 - N50 = 111071204 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145838933-156254668 | [ 1 ] 135423199-145838933 | [ ] 125007465-135423199 | [ ] 114591730-125007464 | [ 2 ] 104175996-114591730 | [ 1 ] 93760262-104175996 | [ ] 83344528-93760262 | [ ] 72928793-83344527 | [ 2 ] 62513059-72928793 | [ ] 52097325-62513059 | [ ] 41681591-52097325 | [ ] 31265856-41681590 | [ 3 ] 20850122-31265856 | [ 6 ] 10434388-20850122 | [ 8 ] 18654-10434388 |************************************************** [ 432 ] Storage Throughput = excellent ( 1409.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40169209 bp ( 40024074 non ambiguous ) - Num Contigs Represented = 107 - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:49 (hh:mm:ss) Elapsed Time Round Time: 00:39:23 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2511 repeats masked totaling 990534 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10051474 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10009060 bp After Masking: 8309158 bp Masked: 16.98 % -- Input Database Coverage: 10051474 bp out of 1193419045 bp ( 0.84 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:13:15 (hh:mm:ss) Elapsed Time, 1095952 HSPs Collected Number of families returned by RECON: 267 Round Time: 00:17:06 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14101 repeats masked totaling 2941840 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30117655 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 30014934 bp After Masking: 24712368 bp Masked: 17.67 % -- Input Database Coverage: 40169129 bp out of 1193419045 bp ( 3.37 % ) Sampling Time: 00:12:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:38:07 (hh:mm:ss) Elapsed Time, 714443 HSPs Collected Number of families returned by RECON: 1454 Round Time: 01:39:08 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38704 repeats masked totaling 9316899 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90168113 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 90003534 bp After Masking: 74560019 bp Masked: 17.16 % -- Input Database Coverage: 130337242 bp out of 1193419045 bp ( 10.92 % ) Sampling Time: 00:37:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:48:25 (hh:mm:ss) Elapsed Time, 52071 HSPs Collected Number of families returned by RECON: 9145 Round Time: 04:33:34 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:39:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134263 repeats masked totaling 31386924 bp(s). - TE Masking time 00:03:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270457470 bp Num Contigs Represented = 267 Non ambiguous bp: Initial: 270007158 bp After Masking: 218845203 bp Masked: 18.95 % -- Input Database Coverage: 400794712 bp out of 1193419045 bp ( 33.58 % ) Sampling Time: 01:56:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 29:57:11 (hh:mm:ss) Elapsed Time, 237131 HSPs Collected Number of families returned by RECON: 61328 Round Time: 32:49:49 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatScout/RECON discovery complete: 444 families found Classification Time: 00:40:00 (hh:mm:ss) Elapsed Time Program Time: 40:39:00 (hh:mm:ss) Elapsed Time