RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EhGq5F/RM_7452.ThuJul41815132024 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: 1720142112 Database = /dev/shm/rModeler.EhGq5F/GCF_000485575.1_Poecilia_formosa-5.1.2 - Sequences = 3985 - Bases = 748923461 - N50 = 1584072 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 6879764-7371162 | [ 3 ] 6388367-6879764 | [ 2 ] 5896970-6388367 | [ 2 ] 5405572-5896969 | [ 3 ] 4914175-5405572 | [ 2 ] 4422778-4914175 | [ 6 ] 3931380-4422777 | [ 4 ] 3439983-3931380 | [ 9 ] 2948586-3439983 | [ 12 ] 2457188-2948585 | [ 23 ] 1965791-2457188 | [ 27 ] 1474394-1965791 | [ 48 ] 982996-1474393 |* [ 74 ] 491599-982996 |** [ 174 ] 202-491599 |************************************************** [ 3596 ] Storage Throughput = excellent ( 1024.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41951334 bp ( 40003212 non ambiguous ) - Num Contigs Represented = 613 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:49 (hh:mm:ss) Elapsed Time Round Time: 00:24:46 (hh:mm:ss) Elapsed Time : 468 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9982 repeats masked totaling 1144034 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10522334 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 10021323 bp After Masking: 8800209 bp Masked: 12.19 % -- Input Database Coverage: 10522334 bp out of 748923461 bp ( 1.40 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 43660 Comparison Time: 00:06:55 (hh:mm:ss) Elapsed Time, 8985 HSPs Collected Number of families returned by RECON: 1602 Round Time: 00:07:48 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32659 repeats masked totaling 4056762 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31469597 bp Num Contigs Represented = 508 Non ambiguous bp: Initial: 30020682 bp After Masking: 25733182 bp Masked: 14.28 % -- Input Database Coverage: 41991931 bp out of 748923461 bp ( 5.61 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 401856 Comparison Time: 00:41:51 (hh:mm:ss) Elapsed Time, 48552 HSPs Collected Number of families returned by RECON: 5217 Round Time: 00:44:57 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112074 repeats masked totaling 14989885 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94266123 bp Num Contigs Represented = 1050 Non ambiguous bp: Initial: 90034176 bp After Masking: 74356130 bp Masked: 17.41 % -- Input Database Coverage: 136258054 bp out of 748923461 bp ( 18.19 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3738745 Comparison Time: 05:19:52 (hh:mm:ss) Elapsed Time, 234562 HSPs Collected Number of families returned by RECON: 17987 Round Time: 05:38:52 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415444 repeats masked totaling 58323007 bp(s). - TE Masking time 00:11:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 283127237 bp Num Contigs Represented = 2065 Non ambiguous bp: Initial: 270011873 bp After Masking: 209537499 bp Masked: 22.40 % -- Input Database Coverage: 419385291 bp out of 748923461 bp ( 56.00 % ) Sampling Time: 00:20:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33812976 Comparison Time: 40:53:03 (hh:mm:ss) Elapsed Time, 622788 HSPs Collected Number of families returned by RECON: 64758 Round Time: 43:06:04 (hh:mm:ss) Elapsed Time : 986 families discovered. RepeatScout/RECON discovery complete: 2020 families found Classification Time: 01:31:20 (hh:mm:ss) Elapsed Time Program Time: 51:33:47 (hh:mm:ss) Elapsed Time