RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zbYJnx/RM_9115.SatMay272052042023 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: 1685245922 Database = /dev/shm/rModeler.zbYJnx/GCF_021461385.2_iqSchPice1.1 - Sequences = 2493 - Bases = 8742459392 - N50 = 991199471 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1171101906-1254751361 | [ 1 ] 1087452452-1171101906 | [ 1 ] 1003802998-1087452452 | [ ] 920153544-1003802998 | [ 2 ] 836504090-920153544 | [ 1 ] 752854636-836504090 | [ ] 669205182-752854636 | [ 1 ] 585555728-669205182 | [ 2 ] 501906274-585555728 | [ 1 ] 418256820-501906274 | [ ] 334607366-418256820 | [ ] 250957912-334607366 | [ ] 167308458-250957912 | [ 2 ] 83659004-167308458 | [ 1 ] 9550-83659004 |************************************************** [ 2481 ] Storage Throughput = excellent ( 1129.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026793 bp ( 40024793 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:16:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:28 (hh:mm:ss) Elapsed Time Round Time: 00:44:37 (hh:mm:ss) Elapsed Time : 768 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13592 repeats masked totaling 4519534 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039904 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10038904 bp After Masking: 4470532 bp Masked: 55.47 % -- Input Database Coverage: 10039904 bp out of 8742459392 bp ( 0.11 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 10518 HSPs Collected Number of families returned by RECON: 1447 Round Time: 00:11:51 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:12:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42780 repeats masked totaling 14399796 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026889 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30025889 bp After Masking: 13642108 bp Masked: 54.57 % -- Input Database Coverage: 40066793 bp out of 8742459392 bp ( 0.46 % ) Sampling Time: 00:15:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:24:58 (hh:mm:ss) Elapsed Time, 54930 HSPs Collected Number of families returned by RECON: 5035 Round Time: 00:42:10 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:36:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136687 repeats masked totaling 44933677 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037587 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 90033587 bp After Masking: 38754375 bp Masked: 56.96 % -- Input Database Coverage: 130104380 bp out of 8742459392 bp ( 1.49 % ) Sampling Time: 00:48:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:13:37 (hh:mm:ss) Elapsed Time, 324749 HSPs Collected Number of families returned by RECON: 14000 Round Time: 03:19:17 (hh:mm:ss) Elapsed Time : 610 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:51:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 481646 repeats masked totaling 157448619 bp(s). - TE Masking time 00:15:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053075 bp Num Contigs Represented = 348 Non ambiguous bp: Initial: 270036331 bp After Masking: 92626112 bp Masked: 65.70 % -- Input Database Coverage: 400157455 bp out of 8742459392 bp ( 4.58 % ) Sampling Time: 02:28:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 13:09:47 (hh:mm:ss) Elapsed Time, 985466 HSPs Collected Number of families returned by RECON: 31595 Round Time: 17:01:11 (hh:mm:ss) Elapsed Time : 1801 families discovered. RepeatScout/RECON discovery complete: 3303 families found Classification Time: 03:26:10 (hh:mm:ss) Elapsed Time Program Time: 25:25:16 (hh:mm:ss) Elapsed Time