RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IQGYmc/RM_33959.TueJan32037152023 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: 1672807034 Database = /dev/shm/rModeler.IQGYmc/GCA_933228915.1_fTelBon1.1 - Sequences = 146 - Bases = 986039709 - N50 = 41802576 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 44854250-48058054 |* [ 3 ] 41650446-44854249 |*** [ 8 ] 38446643-41650446 |*** [ 8 ] 35242839-38446642 |* [ 3 ] 32039036-35242839 | [ 2 ] 28835232-32039035 | [ ] 25631428-28835231 | [ ] 22427625-25631428 | [ ] 19223821-22427624 | [ ] 16020018-19223821 | [ ] 12816214-16020017 | [ ] 9612410-12816213 | [ ] 6408607-9612410 | [ ] 3204803-6408606 | [ ] 1000-3204803 |************************************************** [ 122 ] Storage Throughput = excellent ( 1283.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025205 bp ( 40013849 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:23 (hh:mm:ss) Elapsed Time Round Time: 00:31:26 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5972 repeats masked totaling 1456542 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009501 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10006345 bp After Masking: 6031381 bp Masked: 39.72 % -- Input Database Coverage: 10009501 bp out of 986039709 bp ( 1.02 % ) Sampling Time: 00:09:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 8480 HSPs Collected Number of families returned by RECON: 1011 Round Time: 00:14:57 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18976 repeats masked totaling 4539229 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015693 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30007493 bp After Masking: 19495680 bp Masked: 35.03 % -- Input Database Coverage: 40025194 bp out of 986039709 bp ( 4.06 % ) Sampling Time: 00:21:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:30:40 (hh:mm:ss) Elapsed Time, 79865 HSPs Collected Number of families returned by RECON: 3522 Round Time: 00:53:32 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64120 repeats masked totaling 15783654 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025886 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90001486 bp After Masking: 56023941 bp Masked: 37.75 % -- Input Database Coverage: 130051080 bp out of 986039709 bp ( 13.19 % ) Sampling Time: 01:14:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:11:32 (hh:mm:ss) Elapsed Time, 180150 HSPs Collected Number of families returned by RECON: 11728 Round Time: 04:38:24 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:41:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 235282 repeats masked totaling 57842884 bp(s). - TE Masking time 00:07:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270104941 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270035410 bp After Masking: 156206804 bp Masked: 42.15 % -- Input Database Coverage: 400156021 bp out of 986039709 bp ( 40.58 % ) Sampling Time: 03:55:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 22:38:24 (hh:mm:ss) Elapsed Time, 608077 HSPs Collected Number of families returned by RECON: 43977 Round Time: 27:20:05 (hh:mm:ss) Elapsed Time : 892 families discovered. RepeatScout/RECON discovery complete: 1702 families found Classification Time: 01:37:00 (hh:mm:ss) Elapsed Time Program Time: 35:15:24 (hh:mm:ss) Elapsed Time