RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.S4yGSH/RM_2468819.TueMar190606072024 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: 1710853567 Database = /dev/shm/rModeler.S4yGSH/GCA_036250135.1_bDixPip1.hap2 - Sequences = 595 - Bases = 1027640383 - N50 = 76188976 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146014113-156443622 | [ 1 ] 135584605-146014113 | [ ] 125155097-135584605 | [ ] 114725589-125155097 | [ 2 ] 104296081-114725589 | [ ] 93866573-104296081 | [ ] 83437065-93866573 | [ ] 73007556-83437064 | [ 2 ] 62578048-73007556 | [ 1 ] 52148540-62578048 | [ ] 41719032-52148540 | [ ] 31289524-41719032 | [ 3 ] 20860016-31289524 | [ 5 ] 10430508-20860016 | [ 7 ] 1000-10430508 |************************************************** [ 574 ] Storage Throughput = good ( 814.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034522 bp ( 40032322 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:51 (hh:mm:ss) Elapsed Time Round Time: 00:22:52 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (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... 2388 repeats masked totaling 587374 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016942 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10016142 bp After Masking: 9227975 bp Masked: 7.87 % -- Input Database Coverage: 10016942 bp out of 1027640383 bp ( 0.97 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 1165 HSPs Collected Number of families returned by RECON: 239 Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7141 repeats masked totaling 1822622 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017568 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30016168 bp After Masking: 27183115 bp Masked: 9.44 % -- Input Database Coverage: 40034510 bp out of 1027640383 bp ( 3.90 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:34:48 (hh:mm:ss) Elapsed Time, 8673 HSPs Collected Number of families returned by RECON: 1553 Round Time: 00:38:43 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22242 repeats masked totaling 5583945 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028044 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 90022444 bp After Masking: 81757113 bp Masked: 9.18 % -- Input Database Coverage: 130062554 bp out of 1027640383 bp ( 12.66 % ) Sampling Time: 00:10:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 03:58:32 (hh:mm:ss) Elapsed Time, 56867 HSPs Collected Number of families returned by RECON: 10056 Round Time: 04:11:08 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75557 repeats masked totaling 19591045 bp(s). - TE Masking time 00:02:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023794 bp Num Contigs Represented = 290 Non ambiguous bp: Initial: 270007594 bp After Masking: 242413133 bp Masked: 10.22 % -- Input Database Coverage: 400086348 bp out of 1027640383 bp ( 38.93 % ) Sampling Time: 00:29:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 30:38:38 (hh:mm:ss) Elapsed Time, 205276 HSPs Collected Number of families returned by RECON: 67344 Round Time: 32:30:43 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatScout/RECON discovery complete: 362 families found Classification Time: 00:24:36 (hh:mm:ss) Elapsed Time Program Time: 38:16:22 (hh:mm:ss) Elapsed Time