RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kISCJP/RM_196113.ThuJan51708362023 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: 1672967316 Database = /dev/shm/rModeler.kISCJP/GCF_020740795.1_bApuApu2.pri.cur - Sequences = 110 - Bases = 1100378261 - N50 = 118118700 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 192686075-206448969 | [ 1 ] 178923182-192686075 | [ ] 165160289-178923182 | [ ] 151397395-165160288 | [ 1 ] 137634502-151397395 | [ ] 123871609-137634502 | [ ] 110108715-123871608 |* [ 2 ] 96345822-110108715 | [ ] 82582929-96345822 | [ ] 68820035-82582928 | [ 1 ] 55057142-68820035 | [ 1 ] 41294249-55057142 | [ ] 27531355-41294248 |* [ 2 ] 13768462-27531355 |**** [ 9 ] 5569-13768462 |************************************************** [ 93 ] Storage Throughput = excellent ( 1118.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40087090 bp ( 40034153 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:33 (hh:mm:ss) Elapsed Time Round Time: 00:19:19 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (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... 2293 repeats masked totaling 827240 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041240 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10012881 bp After Masking: 9139143 bp Masked: 8.73 % -- Input Database Coverage: 10041240 bp out of 1100378261 bp ( 0.91 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:39 (hh:mm:ss) Elapsed Time, 461 HSPs Collected Number of families returned by RECON: 223 Round Time: 00:08:50 (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 : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6769 repeats masked totaling 2525110 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045810 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30021232 bp After Masking: 27314378 bp Masked: 9.02 % -- Input Database Coverage: 40087050 bp out of 1100378261 bp ( 3.64 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:54 (hh:mm:ss) Elapsed Time, 5495 HSPs Collected Number of families returned by RECON: 1528 Round Time: 00:30:22 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21469 repeats masked totaling 7657664 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90065324 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90024000 bp After Masking: 81776737 bp Masked: 9.16 % -- Input Database Coverage: 130152374 bp out of 1100378261 bp ( 11.83 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:47:04 (hh:mm:ss) Elapsed Time, 37832 HSPs Collected Number of families returned by RECON: 10521 Round Time: 02:55:14 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74201 repeats masked totaling 25439194 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270441962 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 270020010 bp After Masking: 242629214 bp Masked: 10.14 % -- Input Database Coverage: 400594336 bp out of 1100378261 bp ( 36.41 % ) Sampling Time: 00:20:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 19:19:04 (hh:mm:ss) Elapsed Time, 307233 HSPs Collected Number of families returned by RECON: 70988 Round Time: 20:12:50 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatScout/RECON discovery complete: 334 families found Classification Time: 00:15:12 (hh:mm:ss) Elapsed Time Program Time: 24:21:47 (hh:mm:ss) Elapsed Time