RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sW1H0m/RM_2811723.MonMar251047362024 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: 1711388855 Database = /dev/shm/rModeler.sW1H0m/GCA_947623445.1_kaClaLepa1.1 - Sequences = 103 - Bases = 210089204 - N50 = 25736969 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26869954-28789166 | [ 1 ] 24950743-26869954 |* [ 3 ] 23031532-24950743 | [ 1 ] 21112321-23031532 | [ ] 19193110-21112321 |* [ 3 ] 17273899-19193110 | [ ] 15354688-17273899 | [ 1 ] 13435477-15354688 | [ ] 11516266-13435477 | [ ] 9597055-11516266 | [ ] 7677844-9597055 | [ ] 5758633-7677844 | [ ] 3839422-5758633 | [ ] 1920211-3839422 | [ ] 1000-1920211 |************************************************** [ 94 ] Storage Throughput = excellent ( 1174.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002620 bp ( 40000420 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:30 (hh:mm:ss) Elapsed Time Round Time: 00:22:10 (hh:mm:ss) Elapsed Time : 504 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6544 repeats masked totaling 1512517 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021407 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10021007 bp After Masking: 7081920 bp Masked: 29.33 % -- Input Database Coverage: 10021407 bp out of 210089204 bp ( 4.77 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 4610 HSPs Collected Number of families returned by RECON: 1063 Round Time: 00:07:10 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20203 repeats masked totaling 4551334 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021158 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30019358 bp After Masking: 21072564 bp Masked: 29.80 % -- Input Database Coverage: 40042565 bp out of 210089204 bp ( 19.06 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:29:52 (hh:mm:ss) Elapsed Time, 55779 HSPs Collected Number of families returned by RECON: 3978 Round Time: 00:41:37 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:59 (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... 65921 repeats masked totaling 14628504 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021899 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90016699 bp After Masking: 62148746 bp Masked: 30.96 % -- Input Database Coverage: 130064464 bp out of 210089204 bp ( 61.91 % ) Sampling Time: 00:10:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 02:54:15 (hh:mm:ss) Elapsed Time, 502901 HSPs Collected Number of families returned by RECON: 11742 Round Time: 03:13:22 (hh:mm:ss) Elapsed Time : 465 families discovered. - Increasing sample size to include end piece now = 350046639 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75426 repeats masked totaling 18944342 bp(s). - TE Masking time 00:03:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 80024505 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 80020305 bp After Masking: 48702564 bp Masked: 39.14 % -- Input Database Coverage: 210088969 bp out of 210089204 bp ( 100.00 % ) Sampling Time: 00:33:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2043231 Comparison Time: 02:08:17 (hh:mm:ss) Elapsed Time, 214240 HSPs Collected Number of families returned by RECON: 8159 Round Time: 02:44:21 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatScout/RECON discovery complete: 1189 families found Classification Time: 01:21:25 (hh:mm:ss) Elapsed Time Program Time: 08:30:05 (hh:mm:ss) Elapsed Time