RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.z6Khgd/RM_1018552.FriApr110702412025 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: 1744380160 Database = /data/tmp/rModeler.z6Khgd/GCA_965115925.1_mMyoEma1.hap1.1 - Sequences = 402 - Bases = 2109797427 - N50 = 110124745 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 214663628-229996673 | [ 3 ] 199330583-214663627 | [ ] 183997538-199330582 | [ ] 168664493-183997537 | [ ] 153331448-168664492 | [ ] 137998403-153331447 | [ ] 122665358-137998402 | [ 1 ] 107332314-122665358 | [ 2 ] 91999269-107332313 | [ 3 ] 76666224-91999268 | [ 3 ] 61333179-76666223 | [ 1 ] 46000134-61333178 | [ 5 ] 30667089-46000133 | [ 1 ] 15334044-30667088 | [ 3 ] 1000-15334044 |************************************************** [ 380 ] Storage Throughput = excellent ( 1809.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036182 bp ( 40032086 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:56 (hh:mm:ss) Elapsed Time Round Time: 00:14:23 (hh:mm:ss) Elapsed Time : 374 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14478 repeats masked totaling 2616427 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038731 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10037531 bp After Masking: 6825064 bp Masked: 32.00 % -- Input Database Coverage: 10038731 bp out of 2109797427 bp ( 0.48 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:25 (hh:mm:ss) Elapsed Time, 5174 HSPs Collected Number of families returned by RECON: 851 Round Time: 00:04:20 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44856 repeats masked totaling 8116058 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037371 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30034475 bp After Masking: 19706888 bp Masked: 34.39 % -- Input Database Coverage: 40076102 bp out of 2109797427 bp ( 1.90 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:15:44 (hh:mm:ss) Elapsed Time, 26381 HSPs Collected Number of families returned by RECON: 2391 Round Time: 00:19:01 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144161 repeats masked totaling 26408963 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042228 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90030028 bp After Masking: 57530979 bp Masked: 36.10 % -- Input Database Coverage: 130118330 bp out of 2109797427 bp ( 6.17 % ) Sampling Time: 00:10:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:35:38 (hh:mm:ss) Elapsed Time, 93885 HSPs Collected Number of families returned by RECON: 8506 Round Time: 01:48:20 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474965 repeats masked totaling 87351476 bp(s). - TE Masking time 00:03:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059531 bp Num Contigs Represented = 179 Non ambiguous bp: Initial: 270019379 bp After Masking: 164718387 bp Masked: 39.00 % -- Input Database Coverage: 400177861 bp out of 2109797427 bp ( 18.97 % ) Sampling Time: 00:27:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 10:38:53 (hh:mm:ss) Elapsed Time, 247619 HSPs Collected Number of families returned by RECON: 33018 Round Time: 11:19:12 (hh:mm:ss) Elapsed Time : 449 families discovered. RepeatScout/RECON discovery complete: 1115 families found Classification Time: 00:24:12 (hh:mm:ss) Elapsed Time Program Time: 14:09:28 (hh:mm:ss) Elapsed Time