RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ecZMAx/RM_338776.SunJul200345202025 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: 1753008320 Database = /dev/shm/rModeler.ecZMAx/GCA_964187965.1_klBraLanc2.hap1.1 - Sequences = 122 - Bases = 468418021 - N50 = 24356246 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41740642-44722045 | [ 1 ] 38759239-41740642 | [ 1 ] 35777836-38759239 | [ ] 32796433-35777836 | [ 2 ] 29815030-32796433 | [ ] 26833627-29815030 | [ 1 ] 23852224-26833627 |* [ 3 ] 20870821-23852224 | [ 2 ] 17889418-20870821 |** [ 5 ] 14908015-17889418 |* [ 4 ] 11926612-14908015 | [ ] 8945209-11926612 | [ ] 5963806-8945209 | [ ] 2982403-5963806 | [ ] 1000-2982403 |************************************************** [ 103 ] Storage Throughput = excellent ( 1690.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035455 bp ( 40030655 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:12 (hh:mm:ss) Elapsed Time Round Time: 00:09:26 (hh:mm:ss) Elapsed Time : 826 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14298 repeats masked totaling 2364208 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014835 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10013035 bp After Masking: 6937902 bp Masked: 30.71 % -- Input Database Coverage: 10014835 bp out of 468418021 bp ( 2.14 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:35 (hh:mm:ss) Elapsed Time, 4267 HSPs Collected Number of families returned by RECON: 1023 Round Time: 00:04:17 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44130 repeats masked totaling 7365455 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020540 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30017540 bp After Masking: 20865135 bp Masked: 30.49 % -- Input Database Coverage: 40035375 bp out of 468418021 bp ( 8.55 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:10:53 (hh:mm:ss) Elapsed Time, 37397 HSPs Collected Number of families returned by RECON: 4174 Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135518 repeats masked totaling 22323926 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028788 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90022090 bp After Masking: 62387577 bp Masked: 30.70 % -- Input Database Coverage: 130064163 bp out of 468418021 bp ( 27.77 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:03:41 (hh:mm:ss) Elapsed Time, 277417 HSPs Collected Number of families returned by RECON: 14703 Round Time: 01:12:30 (hh:mm:ss) Elapsed Time : 480 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465777 repeats masked totaling 79828824 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055273 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270028829 bp After Masking: 174683549 bp Masked: 35.31 % -- Input Database Coverage: 400119436 bp out of 468418021 bp ( 85.42 % ) Sampling Time: 00:20:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 07:13:31 (hh:mm:ss) Elapsed Time, 959070 HSPs Collected Number of families returned by RECON: 48790 Round Time: 08:03:27 (hh:mm:ss) Elapsed Time : 1225 families discovered. RepeatScout/RECON discovery complete: 2604 families found Classification Time: 00:59:29 (hh:mm:ss) Elapsed Time Program Time: 10:41:57 (hh:mm:ss) Elapsed Time