RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.byti4G/RM_748979.FriNov150812142024 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: 1731687134 Database = /scratch/tmp/rModeler.byti4G/GCF_039906515.1_mPseCra1.hap1 - Sequences = 438 - Bases = 2674592094 - N50 = 116585307 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185495619-198744646 | [ 2 ] 172246592-185495618 | [ 1 ] 158997566-172246592 | [ ] 145748539-158997565 | [ 2 ] 132499513-145748539 | [ 2 ] 119250486-132499512 | [ ] 106001459-119250485 | [ 5 ] 92752433-106001459 | [ 2 ] 79503406-92752432 | [ 5 ] 66254380-79503406 | [ ] 53005353-66254379 | [ 2 ] 39756326-53005352 | [ ] 26507300-39756326 | [ 1 ] 13258273-26507299 | [ 1 ] 9247-13258273 |************************************************* [ 415 ] Storage Throughput = excellent ( 1552.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039032 bp ( 40038332 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:40 (hh:mm:ss) Elapsed Time Round Time: 00:15:27 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9138 repeats masked totaling 2692871 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035096 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10034696 bp After Masking: 7296429 bp Masked: 27.29 % -- Input Database Coverage: 10035096 bp out of 2674592094 bp ( 0.38 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 111930 HSPs Collected Number of families returned by RECON: 977 Round Time: 00:05:15 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33073 repeats masked totaling 10620752 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003856 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30003556 bp After Masking: 18638878 bp Masked: 37.88 % -- Input Database Coverage: 40038952 bp out of 2674592094 bp ( 1.50 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:11:40 (hh:mm:ss) Elapsed Time, 41427 HSPs Collected Number of families returned by RECON: 2138 Round Time: 00:17:49 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111438 repeats masked totaling 34471470 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90073489 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 90036431 bp After Masking: 53914799 bp Masked: 40.12 % -- Input Database Coverage: 130112441 bp out of 2674592094 bp ( 4.86 % ) Sampling Time: 00:05:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:04:11 (hh:mm:ss) Elapsed Time, 267848 HSPs Collected Number of families returned by RECON: 7422 Round Time: 01:12:06 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 369269 repeats masked totaling 111568478 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270177565 bp Num Contigs Represented = 206 Non ambiguous bp: Initial: 270027310 bp After Masking: 154171503 bp Masked: 42.91 % -- Input Database Coverage: 400290006 bp out of 2674592094 bp ( 14.97 % ) Sampling Time: 00:16:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 07:15:30 (hh:mm:ss) Elapsed Time, 2056072 HSPs Collected Number of families returned by RECON: 30302 Round Time: 07:41:03 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 771 families found Classification Time: 00:15:29 (hh:mm:ss) Elapsed Time Program Time: 09:47:09 (hh:mm:ss) Elapsed Time