RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QouDUr/RM_1672009.WedMar201632432024 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: 1710977563 Database = /dev/shm/rModeler.QouDUr/GCA_036365525.1_sHetFra1.hap1 - Sequences = 2307 - Bases = 6013065386 - N50 = 93226506 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 268750874-287946412 | [ 1 ] 249555336-268750873 | [ ] 230359799-249555336 | [ ] 211164261-230359798 | [ 3 ] 191968724-211164261 | [ 1 ] 172773186-191968723 | [ ] 153577649-172773186 | [ 1 ] 134382111-153577648 | [ 2 ] 115186574-134382111 | [ 5 ] 95991036-115186573 | [ 5 ] 76795499-95991036 | [ 8 ] 57599961-76795498 | [ 9 ] 38404424-57599961 | [ 6 ] 19208886-38404423 | [ 9 ] 13349-19208886 |************************************************** [ 2257 ] Storage Throughput = excellent ( 1268.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40385350 bp ( 40021893 non ambiguous ) - Num Contigs Represented = 232 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:04 (hh:mm:ss) Elapsed Time Round Time: 00:33:43 (hh:mm:ss) Elapsed Time : 607 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14508 repeats masked totaling 4717359 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10103451 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 10019178 bp After Masking: 2144948 bp Masked: 78.59 % -- Input Database Coverage: 10103451 bp out of 6013065386 bp ( 0.17 % ) Sampling Time: 00:12:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:35 (hh:mm:ss) Elapsed Time, 2487 HSPs Collected Number of families returned by RECON: 512 Round Time: 00:16:18 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49559 repeats masked totaling 15623828 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30281897 bp Num Contigs Represented = 193 Non ambiguous bp: Initial: 30002713 bp After Masking: 6836525 bp Masked: 77.21 % -- Input Database Coverage: 40385348 bp out of 6013065386 bp ( 0.67 % ) Sampling Time: 00:33:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:15:15 (hh:mm:ss) Elapsed Time, 18875 HSPs Collected Number of families returned by RECON: 1864 Round Time: 00:49:07 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:35:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145665 repeats masked totaling 46170565 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90559706 bp Num Contigs Represented = 418 Non ambiguous bp: Initial: 90031042 bp After Masking: 19094048 bp Masked: 78.79 % -- Input Database Coverage: 130945054 bp out of 6013065386 bp ( 2.18 % ) Sampling Time: 01:42:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 01:15:07 (hh:mm:ss) Elapsed Time, 102761 HSPs Collected Number of families returned by RECON: 5002 Round Time: 03:02:26 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:40:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 470263 repeats masked totaling 145190088 bp(s). - TE Masking time 00:08:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271130580 bp Num Contigs Represented = 722 Non ambiguous bp: Initial: 270009285 bp After Masking: 52280958 bp Masked: 80.64 % -- Input Database Coverage: 402075634 bp out of 6013065386 bp ( 6.69 % ) Sampling Time: 05:04:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23355195 Comparison Time: 07:03:14 (hh:mm:ss) Elapsed Time, 291616 HSPs Collected Number of families returned by RECON: 13839 Round Time: 12:17:24 (hh:mm:ss) Elapsed Time : 570 families discovered. RepeatScout/RECON discovery complete: 1467 families found Classification Time: 00:57:07 (hh:mm:ss) Elapsed Time Program Time: 17:56:05 (hh:mm:ss) Elapsed Time