RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cFc1IA/RM_6040.SunJan140955292024 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: 1705254928 Database = /dev/shm/rModeler.cFc1IA/GCA_032444005.1_aRanImi1.pri - Sequences = 1673 - Bases = 5956630009 - N50 = 847732560 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1169848561-1253408930 | [ 1 ] 1086288192-1169848560 | [ ] 1002727824-1086288192 | [ ] 919167455-1002727823 | [ ] 835607087-919167455 | [ 2 ] 752046718-835607086 | [ ] 668486349-752046717 | [ 2 ] 584925981-668486349 | [ ] 501365612-584925980 | [ 1 ] 417805244-501365612 | [ ] 334244875-417805243 | [ ] 250684506-334244874 | [ ] 167124138-250684506 | [ 2 ] 83563769-167124137 | [ 2 ] 3401-83563769 |************************************************** [ 1663 ] Storage Throughput = excellent ( 1160.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003719 bp ( 40002715 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:15:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:25 (hh:mm:ss) Elapsed Time Round Time: 00:58:08 (hh:mm:ss) Elapsed Time : 801 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16375 repeats masked totaling 5544639 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026792 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10026388 bp After Masking: 2656464 bp Masked: 73.51 % -- Input Database Coverage: 10026792 bp out of 5956630009 bp ( 0.17 % ) Sampling Time: 00:08:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:53 (hh:mm:ss) Elapsed Time, 23889 HSPs Collected Number of families returned by RECON: 948 Round Time: 00:16:08 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:11:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48077 repeats masked totaling 16210108 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016770 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30016170 bp After Masking: 7706835 bp Masked: 74.32 % -- Input Database Coverage: 40043562 bp out of 5956630009 bp ( 0.67 % ) Sampling Time: 00:23:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:30:35 (hh:mm:ss) Elapsed Time, 59469 HSPs Collected Number of families returned by RECON: 3041 Round Time: 00:56:27 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:35:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163220 repeats masked totaling 52420355 bp(s). - TE Masking time 00:02:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030670 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 90029637 bp After Masking: 21598480 bp Masked: 76.01 % -- Input Database Coverage: 130074232 bp out of 5956630009 bp ( 2.18 % ) Sampling Time: 01:09:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:53:37 (hh:mm:ss) Elapsed Time, 239294 HSPs Collected Number of families returned by RECON: 7384 Round Time: 03:14:45 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:45:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:41:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 523635 repeats masked totaling 166152565 bp(s). - TE Masking time 00:11:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025074 bp Num Contigs Represented = 253 Non ambiguous bp: Initial: 270021166 bp After Masking: 52930231 bp Masked: 80.40 % -- Input Database Coverage: 400099306 bp out of 5956630009 bp ( 6.72 % ) Sampling Time: 03:39:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 13:23:25 (hh:mm:ss) Elapsed Time, 656092 HSPs Collected Number of families returned by RECON: 17396 Round Time: 17:34:49 (hh:mm:ss) Elapsed Time : 978 families discovered. RepeatScout/RECON discovery complete: 2297 families found Classification Time: 01:37:16 (hh:mm:ss) Elapsed Time Program Time: 24:37:33 (hh:mm:ss) Elapsed Time