RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NKbJA5/RM_387688.SatMar91753362024 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: 1710035615 Database = /dev/shm/rModeler.NKbJA5/GCA_022682395.1_HLdesRot8B - Sequences = 430 - Bases = 1976149209 - N50 = 167253561 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197086230-211163384 | [ 3 ] 183009077-197086230 | [ ] 168931924-183009077 | [ 1 ] 154854770-168931923 | [ 2 ] 140777617-154854770 | [ ] 126700464-140777617 | [ 1 ] 112623310-126700463 | [ 2 ] 98546157-112623310 | [ 3 ] 84469004-98546157 | [ 1 ] 70391850-84469003 | [ ] 56314697-70391850 | [ ] 42237544-56314697 | [ ] 28160390-42237543 | [ ] 14083237-28160390 | [ ] 6084-14083237 |************************************************** [ 417 ] Storage Throughput = excellent ( 1126.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021917 bp ( 40015457 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:46 (hh:mm:ss) Elapsed Time Round Time: 00:34:45 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8822 repeats masked totaling 2393585 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006847 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10005847 bp After Masking: 7537170 bp Masked: 24.67 % -- Input Database Coverage: 10006847 bp out of 1976149209 bp ( 0.51 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:37 (hh:mm:ss) Elapsed Time, 52617 HSPs Collected Number of families returned by RECON: 916 Round Time: 00:08:29 (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 : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30848 repeats masked totaling 8015527 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015067 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30009607 bp After Masking: 21703289 bp Masked: 27.68 % -- Input Database Coverage: 40021914 bp out of 1976149209 bp ( 2.03 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:24:54 (hh:mm:ss) Elapsed Time, 24614 HSPs Collected Number of families returned by RECON: 2489 Round Time: 00:28:31 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96635 repeats masked totaling 24456304 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013813 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90004153 bp After Masking: 64843691 bp Masked: 27.95 % -- Input Database Coverage: 130035727 bp out of 1976149209 bp ( 6.58 % ) Sampling Time: 00:07:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:12:25 (hh:mm:ss) Elapsed Time, 78768 HSPs Collected Number of families returned by RECON: 9018 Round Time: 02:22:38 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 326126 repeats masked totaling 82477948 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031326 bp Num Contigs Represented = 160 Non ambiguous bp: Initial: 270004085 bp After Masking: 185359314 bp Masked: 31.35 % -- Input Database Coverage: 400067053 bp out of 1976149209 bp ( 20.24 % ) Sampling Time: 00:25:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 15:00:23 (hh:mm:ss) Elapsed Time, 213829 HSPs Collected Number of families returned by RECON: 39919 Round Time: 15:52:40 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatScout/RECON discovery complete: 853 families found Classification Time: 00:25:34 (hh:mm:ss) Elapsed Time Program Time: 19:52:37 (hh:mm:ss) Elapsed Time