RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0iW4to/RM_22973.FriMay120019502023 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: 1683875989 Database = /dev/shm/rModeler.0iW4to/GCA_028021495.1_fLycPai1.hap1 - Sequences = 461 - Bases = 661271547 - N50 = 28731975 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31910897-34190176 | [ 3 ] 29631619-31910897 | [ 3 ] 27352340-29631618 | [ 6 ] 25073062-27352340 | [ 3 ] 22793784-25073062 | [ 4 ] 20514505-22793783 | [ 2 ] 18235227-20514505 | [ 2 ] 15955948-18235226 | [ ] 13676670-15955948 | [ 1 ] 11397392-13676670 | [ ] 9118113-11397391 | [ ] 6838835-9118113 | [ ] 4559556-6838834 | [ ] 2280278-4559556 | [ ] 1000-2280278 |************************************************** [ 437 ] Storage Throughput = excellent ( 1081.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027927 bp ( 40024527 non ambiguous ) - Num Contigs Represented = 83 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:01 (hh:mm:ss) Elapsed Time Round Time: 00:31:30 (hh:mm:ss) Elapsed Time : 506 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (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... 7303 repeats masked totaling 1360536 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008806 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10008006 bp After Masking: 7957129 bp Masked: 20.49 % -- Input Database Coverage: 10008806 bp out of 661271547 bp ( 1.51 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 11894 HSPs Collected Number of families returned by RECON: 1244 Round Time: 00:08:54 (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 : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23429 repeats masked totaling 4461155 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019041 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30016441 bp After Masking: 23282735 bp Masked: 22.43 % -- Input Database Coverage: 40027847 bp out of 661271547 bp ( 6.05 % ) Sampling Time: 00:05:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:33:11 (hh:mm:ss) Elapsed Time, 93523 HSPs Collected Number of families returned by RECON: 4729 Round Time: 00:40:26 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76958 repeats masked totaling 13953754 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032495 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 90022495 bp After Masking: 69348652 bp Masked: 22.97 % -- Input Database Coverage: 130060342 bp out of 661271547 bp ( 19.67 % ) Sampling Time: 00:17:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:45:02 (hh:mm:ss) Elapsed Time, 350433 HSPs Collected Number of families returned by RECON: 17571 Round Time: 04:16:34 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:43:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 295342 repeats masked totaling 56560766 bp(s). - TE Masking time 00:11:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056373 bp Num Contigs Represented = 276 Non ambiguous bp: Initial: 270024095 bp After Masking: 194451565 bp Masked: 27.99 % -- Input Database Coverage: 400116715 bp out of 661271547 bp ( 60.51 % ) Sampling Time: 00:59:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23430435 Comparison Time: 27:39:54 (hh:mm:ss) Elapsed Time, 2305063 HSPs Collected Number of families returned by RECON: 64722 Round Time: 30:53:01 (hh:mm:ss) Elapsed Time : 1091 families discovered. RepeatScout/RECON discovery complete: 2137 families found Classification Time: 01:51:52 (hh:mm:ss) Elapsed Time Program Time: 38:22:17 (hh:mm:ss) Elapsed Time