RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YD0gqO/RM_4069563.SunFeb232339192025 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: 1740382758 Database = /dev/shm/rModeler.YD0gqO/GCA_965140185.1_bAthNoc1.hap2.1 - Sequences = 660 - Bases = 1302383638 - N50 = 88380324 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 248253446-265985764 | [ 1 ] 230521128-248253445 | [ ] 212788811-230521128 | [ ] 195056493-212788810 | [ ] 177324176-195056493 | [ ] 159591858-177324175 | [ 1 ] 141859540-159591857 | [ ] 124127223-141859540 | [ ] 106394905-124127222 | [ ] 88662588-106394905 | [ 1 ] 70930270-88662587 | [ 2 ] 53197952-70930269 | [ 2 ] 35465635-53197952 | [ 1 ] 17733317-35465634 | [ 8 ] 1000-17733317 |************************************************** [ 644 ] Storage Throughput = excellent ( 1746.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041339 bp ( 40037539 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:49 (hh:mm:ss) Elapsed Time Round Time: 00:11:05 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1524 repeats masked totaling 712714 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020669 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10020069 bp After Masking: 8954428 bp Masked: 10.64 % -- Input Database Coverage: 10020669 bp out of 1302383638 bp ( 0.77 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:11 (hh:mm:ss) Elapsed Time, 571 HSPs Collected Number of families returned by RECON: 260 Round Time: 00:04:06 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4761 repeats masked totaling 2079749 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020655 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30017455 bp After Masking: 26719822 bp Masked: 10.99 % -- Input Database Coverage: 40041324 bp out of 1302383638 bp ( 3.07 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:15:37 (hh:mm:ss) Elapsed Time, 5484 HSPs Collected Number of families returned by RECON: 1446 Round Time: 00:17:24 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15246 repeats masked totaling 6179516 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020217 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 90014895 bp After Masking: 80642844 bp Masked: 10.41 % -- Input Database Coverage: 130061541 bp out of 1302383638 bp ( 9.99 % ) Sampling Time: 00:06:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:34:49 (hh:mm:ss) Elapsed Time, 55680 HSPs Collected Number of families returned by RECON: 8858 Round Time: 01:45:24 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59218 repeats masked totaling 22807035 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044244 bp Num Contigs Represented = 295 Non ambiguous bp: Initial: 270019353 bp After Masking: 236524136 bp Masked: 12.40 % -- Input Database Coverage: 400105785 bp out of 1302383638 bp ( 30.72 % ) Sampling Time: 00:18:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 12:02:43 (hh:mm:ss) Elapsed Time, 322175 HSPs Collected Number of families returned by RECON: 53795 Round Time: 12:39:43 (hh:mm:ss) Elapsed Time : 284 families discovered. RepeatScout/RECON discovery complete: 449 families found Classification Time: 00:36:04 (hh:mm:ss) Elapsed Time Program Time: 15:33:46 (hh:mm:ss) Elapsed Time