RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.reXsli/RM_3024980.FriMar151130352024 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: 1710527434 Database = /dev/shm/rModeler.reXsli/GCA_036010745.1_bCalNic1.hap2 - Sequences = 226 - Bases = 1197404482 - N50 = 123281365 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201335655-215715690 | [ 1 ] 186955621-201335655 | [ ] 172575587-186955621 | [ ] 158195552-172575586 | [ 1 ] 143815518-158195552 | [ ] 129435484-143815518 | [ ] 115055449-129435483 | [ 1 ] 100675415-115055449 | [ 1 ] 86295381-100675415 | [ ] 71915346-86295380 | [ 1 ] 57535312-71915346 | [ 1 ] 43155278-57535312 | [ 1 ] 28775243-43155277 | [ 1 ] 14395209-28775243 |** [ 9 ] 15175-14395209 |************************************************** [ 209 ] Storage Throughput = excellent ( 1087.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014035 bp ( 40013635 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:47 (hh:mm:ss) Elapsed Time Round Time: 00:20:13 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3029 repeats masked totaling 753149 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004263 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10004263 bp After Masking: 8987640 bp Masked: 10.16 % -- Input Database Coverage: 10004263 bp out of 1197404482 bp ( 0.84 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 2475 HSPs Collected Number of families returned by RECON: 225 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8137 repeats masked totaling 2437143 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009692 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30009292 bp After Masking: 26822304 bp Masked: 10.62 % -- Input Database Coverage: 40013955 bp out of 1197404482 bp ( 3.34 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:35:03 (hh:mm:ss) Elapsed Time, 13371 HSPs Collected Number of families returned by RECON: 1340 Round Time: 00:41:21 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27530 repeats masked totaling 7767620 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006502 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90005402 bp After Masking: 79928293 bp Masked: 11.20 % -- Input Database Coverage: 130020457 bp out of 1197404482 bp ( 10.86 % ) Sampling Time: 00:16:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:43:01 (hh:mm:ss) Elapsed Time, 47291 HSPs Collected Number of families returned by RECON: 8053 Round Time: 04:04:15 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94985 repeats masked totaling 27144458 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025078 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270019778 bp After Masking: 236737311 bp Masked: 12.33 % -- Input Database Coverage: 400045535 bp out of 1197404482 bp ( 33.41 % ) Sampling Time: 00:54:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 29:10:18 (hh:mm:ss) Elapsed Time, 205825 HSPs Collected Number of families returned by RECON: 53469 Round Time: 30:36:12 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 424 families found Classification Time: 00:30:53 (hh:mm:ss) Elapsed Time Program Time: 36:21:19 (hh:mm:ss) Elapsed Time