RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.kquGaV/RM_216447.SunApr201149012025 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: 1745174941 Database = /data/tmp/rModeler.kquGaV/GCF_048164855.1_mCanLup2.hap1 - Sequences = 249 - Bases = 2495589887 - N50 = 65588690 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116887328-125236116 | [ 2 ] 108538540-116887327 | [ ] 100189752-108538539 | [ ] 91840964-100189751 | [ 1 ] 83492177-91840964 | [ 3 ] 75143389-83492176 |* [ 5 ] 66794601-75143388 | [ 2 ] 58445813-66794600 |* [ 8 ] 50097025-58445812 |* [ 5 ] 41748238-50097025 |* [ 8 ] 33399450-41748237 | [ 2 ] 25050662-33399449 | [ 3 ] 16701874-25050661 | [ ] 8353086-16701873 | [ 1 ] 4299-8353086 |************************************************** [ 209 ] Storage Throughput = excellent ( 1008.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029105 bp ( 40028705 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:35 (hh:mm:ss) Elapsed Time Round Time: 00:26:59 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13553 repeats masked totaling 2583256 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001490 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10001490 bp After Masking: 7313106 bp Masked: 26.88 % -- Input Database Coverage: 10001490 bp out of 2495589887 bp ( 0.40 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 6052 HSPs Collected Number of families returned by RECON: 877 Round Time: 00:07:33 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42188 repeats masked totaling 8179276 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027603 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30027203 bp After Masking: 21481399 bp Masked: 28.46 % -- Input Database Coverage: 40029093 bp out of 2495589887 bp ( 1.60 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:58 (hh:mm:ss) Elapsed Time, 38484 HSPs Collected Number of families returned by RECON: 2592 Round Time: 00:37:51 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134668 repeats masked totaling 26701449 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011387 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90010987 bp After Masking: 61905125 bp Masked: 31.22 % -- Input Database Coverage: 130040480 bp out of 2495589887 bp ( 5.21 % ) Sampling Time: 00:11:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:44:14 (hh:mm:ss) Elapsed Time, 1506975 HSPs Collected Number of families returned by RECON: 8981 Round Time: 04:11:10 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 453931 repeats masked totaling 88360435 bp(s). - TE Masking time 00:06:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021246 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 270019045 bp After Masking: 177628751 bp Masked: 34.22 % -- Input Database Coverage: 400061726 bp out of 2495589887 bp ( 16.03 % ) Sampling Time: 00:34:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 25:37:11 (hh:mm:ss) Elapsed Time, 14369856 HSPs Collected Number of families returned by RECON: 37197 Round Time: 27:22:42 (hh:mm:ss) Elapsed Time : 341 families discovered. RepeatScout/RECON discovery complete: 760 families found Classification Time: 00:30:20 (hh:mm:ss) Elapsed Time Program Time: 33:16:35 (hh:mm:ss) Elapsed Time