RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HYMsr7/RM_2256554.SunMar101625482024 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: 1710113148 Database = /dev/shm/rModeler.HYMsr7/GCA_026230045.1_mCorTow1.0.hap2 - Sequences = 182 - Bases = 1961562149 - N50 = 186673231 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 221591269-237418211 | [ 2 ] 205764328-221591269 | [ 1 ] 189937387-205764328 | [ ] 174110445-189937386 | [ 2 ] 158283504-174110445 | [ 2 ] 142456563-158283504 | [ 1 ] 126629621-142456562 | [ ] 110802680-126629621 | [ ] 94975739-110802680 | [ 1 ] 79148797-94975738 | [ ] 63321856-79148797 | [ ] 47494915-63321856 | [ 3 ] 31667973-47494914 | [ 1 ] 15841032-31667973 |* [ 4 ] 14091-15841032 |************************************************** [ 165 ] Storage Throughput = excellent ( 1363.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006963 bp ( 40006463 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:52 (hh:mm:ss) Elapsed Time Round Time: 00:26:33 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13868 repeats masked totaling 2817223 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006329 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10006229 bp After Masking: 7064238 bp Masked: 29.40 % -- Input Database Coverage: 10006329 bp out of 1961562149 bp ( 0.51 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:10 (hh:mm:ss) Elapsed Time, 5359 HSPs Collected Number of families returned by RECON: 817 Round Time: 00:07:04 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44352 repeats masked totaling 8909471 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000633 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30000233 bp After Masking: 20440747 bp Masked: 31.86 % -- Input Database Coverage: 40006962 bp out of 1961562149 bp ( 2.04 % ) Sampling Time: 00:05:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:26:03 (hh:mm:ss) Elapsed Time, 140587 HSPs Collected Number of families returned by RECON: 2427 Round Time: 00:32:33 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138149 repeats masked totaling 27969745 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040058 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90038958 bp After Masking: 60443017 bp Masked: 32.87 % -- Input Database Coverage: 130047020 bp out of 1961562149 bp ( 6.63 % ) Sampling Time: 00:14:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:36:11 (hh:mm:ss) Elapsed Time, 336616 HSPs Collected Number of families returned by RECON: 8825 Round Time: 02:54:29 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459721 repeats masked totaling 92143776 bp(s). - TE Masking time 00:05:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024624 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270021014 bp After Masking: 173600322 bp Masked: 35.71 % -- Input Database Coverage: 400071644 bp out of 1961562149 bp ( 20.40 % ) Sampling Time: 00:43:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 21:35:20 (hh:mm:ss) Elapsed Time, 2053042 HSPs Collected Number of families returned by RECON: 36526 Round Time: 22:50:26 (hh:mm:ss) Elapsed Time : 444 families discovered. RepeatScout/RECON discovery complete: 1048 families found Classification Time: 00:45:10 (hh:mm:ss) Elapsed Time Program Time: 27:36:15 (hh:mm:ss) Elapsed Time