RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kW6snQ/RM_27898.TueJul161514102024 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: 1721168044 Database = /dev/shm/rModeler.kW6snQ/GCF_011125445.2_MU-UCD_Fhet_4.1 - Sequences = 1031 - Bases = 1203505739 - N50 = 39656907 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 45988309-49273114 | [ 3 ] 42703504-45988308 | [ 3 ] 39418699-42703503 | [ 7 ] 36133894-39418698 | [ 3 ] 32849090-36133894 | [ 5 ] 29564285-32849089 | [ 1 ] 26279480-29564284 | [ 1 ] 22994675-26279479 | [ 1 ] 19709870-22994674 | [ ] 16425066-19709870 | [ ] 13140261-16425065 | [ ] 9855456-13140260 | [ ] 6570651-9855455 | [ ] 3285846-6570650 | [ 8 ] 1042-3285846 |************************************************** [ 999 ] Storage Throughput = excellent ( 1036.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40054141 bp ( 40003161 non ambiguous ) - Num Contigs Represented = 182 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:43 (hh:mm:ss) Elapsed Time Round Time: 00:39:15 (hh:mm:ss) Elapsed Time : 868 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14721 repeats masked totaling 3052435 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016279 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10008782 bp After Masking: 6735849 bp Masked: 32.70 % -- Input Database Coverage: 10016279 bp out of 1203505739 bp ( 0.83 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:31:04 (hh:mm:ss) Elapsed Time, 8566 HSPs Collected Number of families returned by RECON: 1613 Round Time: 00:33:36 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45325 repeats masked totaling 9353179 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30077847 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 30034364 bp After Masking: 20040454 bp Masked: 33.27 % -- Input Database Coverage: 40094126 bp out of 1203505739 bp ( 3.33 % ) Sampling Time: 00:02:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 01:52:14 (hh:mm:ss) Elapsed Time, 51497 HSPs Collected Number of families returned by RECON: 5115 Round Time: 02:01:33 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152951 repeats masked totaling 30502310 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90121107 bp Num Contigs Represented = 282 Non ambiguous bp: Initial: 90015289 bp After Masking: 57501951 bp Masked: 36.12 % -- Input Database Coverage: 130215233 bp out of 1203505739 bp ( 10.82 % ) Sampling Time: 00:09:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 07:39:51 (hh:mm:ss) Elapsed Time, 293126 HSPs Collected Number of families returned by RECON: 14861 Round Time: 08:16:20 (hh:mm:ss) Elapsed Time : 589 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536353 repeats masked totaling 110190968 bp(s). - TE Masking time 00:16:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270344322 bp Num Contigs Represented = 618 Non ambiguous bp: Initial: 270033814 bp After Masking: 153655850 bp Masked: 43.10 % -- Input Database Coverage: 400559555 bp out of 1203505739 bp ( 33.28 % ) Sampling Time: 00:34:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23780856 Comparison Time: 46:23:25 (hh:mm:ss) Elapsed Time, 754438 HSPs Collected Number of families returned by RECON: 43618 Round Time: 48:28:42 (hh:mm:ss) Elapsed Time : 1221 families discovered. RepeatScout/RECON discovery complete: 2844 families found Classification Time: 02:22:19 (hh:mm:ss) Elapsed Time Program Time: 62:21:45 (hh:mm:ss) Elapsed Time