RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uhNLSM/RM_49092.SunMar300229002025 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: 1743326939 Database = /dev/shm/rModeler.uhNLSM/GCA_048569465.1_aAnoBae1.hap2 - Sequences = 2426 - Bases = 6129031283 - N50 = 713880292 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 909941438-974936910 | [ 1 ] 844945966-909941437 | [ ] 779950495-844945966 | [ 1 ] 714955023-779950494 | [ ] 649959552-714955023 | [ 2 ] 584964080-649959551 | [ 1 ] 519968609-584964080 | [ 1 ] 454973137-519968608 | [ ] 389977666-454973137 | [ ] 324982194-389977665 | [ ] 259986723-324982194 | [ 2 ] 194991251-259986722 | [ 2 ] 129995780-194991251 | [ 2 ] 65000308-129995779 | [ ] 4837-65000308 |************************************************** [ 2414 ] Storage Throughput = excellent ( 1947.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011239 bp ( 40005539 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:05:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:53 (hh:mm:ss) Elapsed Time Round Time: 00:19:23 (hh:mm:ss) Elapsed Time : 1023 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17134 repeats masked totaling 5655076 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035206 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10033806 bp After Masking: 2863875 bp Masked: 71.46 % -- Input Database Coverage: 10035206 bp out of 6129031283 bp ( 0.16 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:41 (hh:mm:ss) Elapsed Time, 18857 HSPs Collected Number of families returned by RECON: 1031 Round Time: 00:05:32 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51427 repeats masked totaling 17351621 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015953 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 30011653 bp After Masking: 7924341 bp Masked: 73.60 % -- Input Database Coverage: 40051159 bp out of 6129031283 bp ( 0.65 % ) Sampling Time: 00:08:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:09:35 (hh:mm:ss) Elapsed Time, 48350 HSPs Collected Number of families returned by RECON: 3185 Round Time: 00:19:04 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 166422 repeats masked totaling 52297059 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014042 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 90002842 bp After Masking: 22841837 bp Masked: 74.62 % -- Input Database Coverage: 130065201 bp out of 6129031283 bp ( 2.12 % ) Sampling Time: 00:26:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 00:42:10 (hh:mm:ss) Elapsed Time, 240949 HSPs Collected Number of families returned by RECON: 8080 Round Time: 01:12:21 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 557569 repeats masked totaling 169947959 bp(s). - TE Masking time 00:04:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048336 bp Num Contigs Represented = 418 Non ambiguous bp: Initial: 270016057 bp After Masking: 56124442 bp Masked: 79.21 % -- Input Database Coverage: 400113537 bp out of 6129031283 bp ( 6.53 % ) Sampling Time: 01:22:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 03:34:18 (hh:mm:ss) Elapsed Time, 671901 HSPs Collected Number of families returned by RECON: 18808 Round Time: 05:07:03 (hh:mm:ss) Elapsed Time : 1004 families discovered. RepeatScout/RECON discovery complete: 2594 families found Classification Time: 00:53:36 (hh:mm:ss) Elapsed Time Program Time: 07:56:59 (hh:mm:ss) Elapsed Time