RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3HUBVv/RM_28053.WedJan101934542024 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: 1704944094 Database = /dev/shm/rModeler.3HUBVv/GCA_020801775.1_bPorHoc1.pat.decon - Sequences = 178 - Bases = 1245128614 - N50 = 77818260 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 157531149-168782532 | [ 1 ] 146279767-157531149 | [ ] 135028385-146279767 | [ ] 123777002-135028384 | [ 1 ] 112525620-123777002 | [ ] 101274238-112525620 | [ ] 90022855-101274237 | [ 1 ] 78771473-90022855 | [ 1 ] 67520091-78771473 | [ 2 ] 56268708-67520090 | [ 1 ] 45017326-56268708 | [ 1 ] 33765944-45017326 |* [ 4 ] 22514561-33765943 |* [ 4 ] 11263179-22514561 |** [ 8 ] 11797-11263179 |************************************************** [ 154 ] Storage Throughput = excellent ( 1126.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40488822 bp ( 40030492 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:51 (hh:mm:ss) Elapsed Time Round Time: 00:27:43 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3325 repeats masked totaling 1044383 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10106334 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10026258 bp After Masking: 8665657 bp Masked: 13.57 % -- Input Database Coverage: 10106334 bp out of 1245128614 bp ( 0.81 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 2665 HSPs Collected Number of families returned by RECON: 295 Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10651 repeats masked totaling 3432407 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30382480 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30004226 bp After Masking: 25537602 bp Masked: 14.89 % -- Input Database Coverage: 40488814 bp out of 1245128614 bp ( 3.25 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:32:47 (hh:mm:ss) Elapsed Time, 7752 HSPs Collected Number of families returned by RECON: 1282 Round Time: 00:36:25 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31475 repeats masked totaling 10039266 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90630715 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90014736 bp After Masking: 76765657 bp Masked: 14.72 % -- Input Database Coverage: 131119529 bp out of 1245128614 bp ( 10.53 % ) Sampling Time: 00:09:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 04:05:46 (hh:mm:ss) Elapsed Time, 39931 HSPs Collected Number of families returned by RECON: 8225 Round Time: 04:17:11 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99860 repeats masked totaling 31668954 bp(s). - TE Masking time 00:03:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272606616 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 270010978 bp After Masking: 226920374 bp Masked: 15.96 % -- Input Database Coverage: 403726145 bp out of 1245128614 bp ( 32.42 % ) Sampling Time: 00:33:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 33:52:30 (hh:mm:ss) Elapsed Time, 240906 HSPs Collected Number of families returned by RECON: 56933 Round Time: 35:14:26 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatScout/RECON discovery complete: 335 families found Classification Time: 00:32:44 (hh:mm:ss) Elapsed Time Program Time: 41:16:49 (hh:mm:ss) Elapsed Time