RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IMKrJd/RM_6926.MonJul10516142024 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: 1719836174 Database = /dev/shm/rModeler.IMKrJd/GCA_023055335.1_fCliAna1.0.p - Sequences = 443 - Bases = 538118947 - N50 = 21652950 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 23820948-25521869 | [ 4 ] 22120027-23820947 | [ 4 ] 20419107-22120027 | [ 4 ] 18718186-20419106 | [ 3 ] 17017266-18718186 | [ 3 ] 15316345-17017265 | [ 2 ] 13615424-15316344 | [ 1 ] 11914504-13615424 | [ 1 ] 10213583-11914503 | [ 2 ] 8512663-10213583 | [ ] 6811742-8512662 | [ 1 ] 5110821-6811741 | [ ] 3409901-5110821 | [ 3 ] 1708980-3409900 | [ 4 ] 8060-1708980 |************************************************* [ 411 ] Storage Throughput = excellent ( 1044.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003240 bp ( 40002040 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:57 (hh:mm:ss) Elapsed Time Round Time: 00:26:33 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3688 repeats masked totaling 494037 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036419 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10036219 bp After Masking: 8882605 bp Masked: 11.49 % -- Input Database Coverage: 10036419 bp out of 538118947 bp ( 1.87 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:28 (hh:mm:ss) Elapsed Time, 11536 HSPs Collected Number of families returned by RECON: 1278 Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11562 repeats masked totaling 1778317 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006899 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30005899 bp After Masking: 26138659 bp Masked: 12.89 % -- Input Database Coverage: 40043318 bp out of 538118947 bp ( 7.44 % ) Sampling Time: 00:03:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:31:59 (hh:mm:ss) Elapsed Time, 45766 HSPs Collected Number of families returned by RECON: 4672 Round Time: 00:36:43 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46087 repeats masked totaling 6697119 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024880 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 90021180 bp After Masking: 76938952 bp Masked: 14.53 % -- Input Database Coverage: 130068198 bp out of 538118947 bp ( 24.17 % ) Sampling Time: 00:10:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 03:56:29 (hh:mm:ss) Elapsed Time, 178790 HSPs Collected Number of families returned by RECON: 17920 Round Time: 04:18:44 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 190272 repeats masked totaling 28036898 bp(s). - TE Masking time 00:06:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046655 bp Num Contigs Represented = 286 Non ambiguous bp: Initial: 270035155 bp After Masking: 223290648 bp Masked: 17.31 % -- Input Database Coverage: 400114853 bp out of 538118947 bp ( 74.35 % ) Sampling Time: 00:35:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23629375 Comparison Time: 37:15:41 (hh:mm:ss) Elapsed Time, 624520 HSPs Collected Number of families returned by RECON: 74862 Round Time: 39:58:27 (hh:mm:ss) Elapsed Time : 842 families discovered. RepeatScout/RECON discovery complete: 1562 families found Classification Time: 00:58:23 (hh:mm:ss) Elapsed Time Program Time: 46:25:44 (hh:mm:ss) Elapsed Time