RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fPrDjG/RM_372409.TueJan30543232023 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: 1672753402 Database = /dev/shm/rModeler.fPrDjG/GCF_007364275.1_fArcCen1 - Sequences = 188 - Bases = 932930362 - N50 = 35997201 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 40590426-43489282 | [ 2 ] 37691571-40590426 |* [ 5 ] 34792716-37691571 |** [ 7 ] 31893860-34792715 | [ 1 ] 28995005-31893860 |* [ 5 ] 26096150-28995005 | [ 2 ] 23197294-26096149 | [ 2 ] 20298439-23197294 | [ ] 17399584-20298439 | [ ] 14500728-17399583 | [ ] 11601873-14500728 | [ ] 8703018-11601873 | [ 1 ] 5804162-8703017 | [ 2 ] 2905307-5804162 |*** [ 10 ] 6452-2905307 |************************************************** [ 151 ] Storage Throughput = excellent ( 1536.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40815671 bp ( 40023219 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:28 (hh:mm:ss) Elapsed Time Round Time: 00:15:50 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11594 repeats masked totaling 2550930 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10334042 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10028367 bp After Masking: 7290292 bp Masked: 27.30 % -- Input Database Coverage: 10334042 bp out of 932930362 bp ( 1.11 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 6340 HSPs Collected Number of families returned by RECON: 1284 Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (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... 34981 repeats masked totaling 7900604 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30561701 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30034755 bp After Masking: 21622597 bp Masked: 28.01 % -- Input Database Coverage: 40895743 bp out of 932930362 bp ( 4.38 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:24:33 (hh:mm:ss) Elapsed Time, 38227 HSPs Collected Number of families returned by RECON: 4707 Round Time: 00:27:29 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114412 repeats masked totaling 24906036 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91969503 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90033579 bp After Masking: 63807266 bp Masked: 29.13 % -- Input Database Coverage: 132865246 bp out of 932930362 bp ( 14.24 % ) Sampling Time: 00:05:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2657665 Comparison Time: 02:20:48 (hh:mm:ss) Elapsed Time, 222687 HSPs Collected Number of families returned by RECON: 16079 Round Time: 02:32:55 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 401434 repeats masked totaling 88201977 bp(s). - TE Masking time 00:05:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275182731 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270038206 bp After Masking: 177908039 bp Masked: 34.12 % -- Input Database Coverage: 408047977 bp out of 932930362 bp ( 43.74 % ) Sampling Time: 00:18:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23856778 Comparison Time: 15:55:59 (hh:mm:ss) Elapsed Time, 724496 HSPs Collected Number of families returned by RECON: 59999 Round Time: 17:15:36 (hh:mm:ss) Elapsed Time : 1191 families discovered. RepeatScout/RECON discovery complete: 2357 families found Classification Time: 01:33:49 (hh:mm:ss) Elapsed Time Program Time: 22:12:30 (hh:mm:ss) Elapsed Time