RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qLtVxU/RM_27197.SunJul140243582024 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: 1720950236 Database = /dev/shm/rModeler.qLtVxU/GCF_004354835.1_PFLA_1.0 - Sequences = 268 - Bases = 877456336 - N50 = 37816349 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41608910-44580961 | [ 4 ] 38636860-41608910 | [ 4 ] 35664810-38636860 |* [ 5 ] 32692760-35664810 |* [ 7 ] 29720710-32692760 | [ 1 ] 26748660-29720710 | [ 2 ] 23776610-26748660 | [ ] 20804560-23776610 | [ ] 17832510-20804560 | [ 1 ] 14860460-17832510 | [ ] 11888410-14860460 | [ ] 8916360-11888410 | [ ] 5944310-8916360 | [ ] 2972260-5944310 | [ ] 210-2972260 |************************************************** [ 244 ] Storage Throughput = excellent ( 1034.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40046099 bp ( 40026357 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:29 (hh:mm:ss) Elapsed Time Round Time: 00:31:06 (hh:mm:ss) Elapsed Time : 1071 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14140 repeats masked totaling 2386311 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10044697 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10038455 bp After Masking: 7056871 bp Masked: 29.70 % -- Input Database Coverage: 10044697 bp out of 877456336 bp ( 1.14 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:17 (hh:mm:ss) Elapsed Time, 16975 HSPs Collected Number of families returned by RECON: 1640 Round Time: 00:08:40 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43734 repeats masked totaling 7453711 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041391 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30027891 bp After Masking: 20828175 bp Masked: 30.64 % -- Input Database Coverage: 40086088 bp out of 877456336 bp ( 4.57 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:17 (hh:mm:ss) Elapsed Time, 54295 HSPs Collected Number of families returned by RECON: 5551 Round Time: 00:39:29 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140500 repeats masked totaling 23562065 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040820 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90004149 bp After Masking: 60772113 bp Masked: 32.48 % -- Input Database Coverage: 130126908 bp out of 877456336 bp ( 14.83 % ) Sampling Time: 00:17:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:31:10 (hh:mm:ss) Elapsed Time, 356364 HSPs Collected Number of families returned by RECON: 16991 Round Time: 04:07:30 (hh:mm:ss) Elapsed Time : 798 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 511309 repeats masked totaling 88159105 bp(s). - TE Masking time 00:16:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270160338 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 270034350 bp After Masking: 165748710 bp Masked: 38.62 % -- Input Database Coverage: 400287246 bp out of 877456336 bp ( 45.62 % ) Sampling Time: 01:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 25:31:27 (hh:mm:ss) Elapsed Time, 842459 HSPs Collected Number of families returned by RECON: 54995 Round Time: 28:41:45 (hh:mm:ss) Elapsed Time : 1623 families discovered. RepeatScout/RECON discovery complete: 3637 families found Classification Time: 02:18:18 (hh:mm:ss) Elapsed Time Program Time: 36:26:48 (hh:mm:ss) Elapsed Time