RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kiLmDR/RM_2557.FriJan120506572024 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: 1705064815 Database = /dev/shm/rModeler.kiLmDR/GCA_027789765.1_aDenEbr1.pat - Sequences = 2200 - Bases = 2214937069 - N50 = 163017972 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 218804114-234432908 | [ 2 ] 203175320-218804113 | [ ] 187546527-203175320 | [ 1 ] 171917733-187546526 | [ 1 ] 156288940-171917733 | [ 1 ] 140660146-156288939 | [ 2 ] 125031353-140660146 | [ 1 ] 109402559-125031352 | [ 1 ] 93773766-109402559 | [ 2 ] 78144972-93773765 | [ 3 ] 62516179-78144972 | [ 1 ] 46887385-62516178 | [ ] 31258592-46887385 | [ ] 15629798-31258591 | [ ] 1005-15629798 |************************************************** [ 2185 ] Storage Throughput = excellent ( 1126.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078270 bp ( 40027374 non ambiguous ) - Num Contigs Represented = 89 - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:33 (hh:mm:ss) Elapsed Time Round Time: 00:32:48 (hh:mm:ss) Elapsed Time : 944 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20643 repeats masked totaling 3780563 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10061455 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10021355 bp After Masking: 4745688 bp Masked: 52.64 % -- Input Database Coverage: 10061455 bp out of 2214937069 bp ( 0.45 % ) Sampling Time: 00:04:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 19055 HSPs Collected Number of families returned by RECON: 1432 Round Time: 00:10:35 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65294 repeats masked totaling 12107359 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016735 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30005939 bp After Masking: 13853485 bp Masked: 53.83 % -- Input Database Coverage: 40078190 bp out of 2214937069 bp ( 1.81 % ) Sampling Time: 00:09:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:27:48 (hh:mm:ss) Elapsed Time, 77316 HSPs Collected Number of families returned by RECON: 4935 Round Time: 00:39:34 (hh:mm:ss) Elapsed Time : 148 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 206498 repeats masked totaling 37522544 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90125824 bp Num Contigs Represented = 182 Non ambiguous bp: Initial: 90039483 bp After Masking: 38671887 bp Masked: 57.05 % -- Input Database Coverage: 130204014 bp out of 2214937069 bp ( 5.88 % ) Sampling Time: 00:37:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2627778 Comparison Time: 03:16:58 (hh:mm:ss) Elapsed Time, 269007 HSPs Collected Number of families returned by RECON: 12910 Round Time: 04:09:42 (hh:mm:ss) Elapsed Time : 509 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:26:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 685991 repeats masked totaling 125885124 bp(s). - TE Masking time 00:13:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270796804 bp Num Contigs Represented = 480 Non ambiguous bp: Initial: 270002629 bp After Masking: 104311694 bp Masked: 61.37 % -- Input Database Coverage: 401000818 bp out of 2214937069 bp ( 18.10 % ) Sampling Time: 02:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23870595 Comparison Time: 25:56:47 (hh:mm:ss) Elapsed Time, 779882 HSPs Collected Number of families returned by RECON: 35890 Round Time: 29:19:47 (hh:mm:ss) Elapsed Time : 1356 families discovered. RepeatScout/RECON discovery complete: 2985 families found Classification Time: 01:37:35 (hh:mm:ss) Elapsed Time Program Time: 36:30:01 (hh:mm:ss) Elapsed Time