RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RRf3Vz/RM_688750.ThuMar212112362024 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: 1711080755 Database = /dev/shm/rModeler.RRf3Vz/GCA_036417535.1_bChlMac1.mat - Sequences = 329 - Bases = 1273933319 - N50 = 84738614 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201314742-215693158 | [ 1 ] 186936326-201314742 | [ ] 172557910-186936326 | [ ] 158179494-172557910 | [ 1 ] 143801078-158179494 | [ ] 129422662-143801078 | [ ] 115044246-129422662 | [ 1 ] 100665830-115044246 | [ ] 86287414-100665830 | [ ] 71908998-86287414 | [ 3 ] 57530582-71908998 | [ ] 43152166-57530582 | [ 2 ] 28773750-43152166 | [ 2 ] 14395334-28773750 |* [ 9 ] 16918-14395334 |************************************************** [ 310 ] Storage Throughput = excellent ( 1031.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036210 bp ( 40035810 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:08 (hh:mm:ss) Elapsed Time Round Time: 00:25:06 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2611 repeats masked totaling 1174056 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034676 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10034676 bp After Masking: 8496980 bp Masked: 15.32 % -- Input Database Coverage: 10034676 bp out of 1273933319 bp ( 0.79 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:09:37 (hh:mm:ss) Elapsed Time, 8964 HSPs Collected Number of families returned by RECON: 231 Round Time: 00:11:16 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6606 repeats masked totaling 2941213 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001454 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30001054 bp After Masking: 25445140 bp Masked: 15.19 % -- Input Database Coverage: 40036130 bp out of 1273933319 bp ( 3.14 % ) Sampling Time: 00:08:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:37:17 (hh:mm:ss) Elapsed Time, 13937 HSPs Collected Number of families returned by RECON: 1241 Round Time: 00:46:03 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19910 repeats masked totaling 8220822 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027576 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90026176 bp After Masking: 77967085 bp Masked: 13.40 % -- Input Database Coverage: 130063706 bp out of 1273933319 bp ( 10.21 % ) Sampling Time: 00:15:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 04:00:41 (hh:mm:ss) Elapsed Time, 117434 HSPs Collected Number of families returned by RECON: 7782 Round Time: 04:20:35 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69718 repeats masked totaling 27188981 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021005 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 270016205 bp After Masking: 230156878 bp Masked: 14.76 % -- Input Database Coverage: 400084711 bp out of 1273933319 bp ( 31.41 % ) Sampling Time: 00:48:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23021505 Comparison Time: 33:12:09 (hh:mm:ss) Elapsed Time, 2085131 HSPs Collected Number of families returned by RECON: 50060 Round Time: 34:30:19 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatScout/RECON discovery complete: 323 families found Classification Time: 00:25:16 (hh:mm:ss) Elapsed Time Program Time: 40:38:35 (hh:mm:ss) Elapsed Time