RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.GZuNsf/RM_3926342.WedDec181108282024 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: 1734548907 Database = /data/tmp/rModeler.GZuNsf/GCA_039906465.1_bAegAlb1.hap2 - Sequences = 525 - Bases = 1051698180 - N50 = 57102674 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 102862435-110209432 | [ 1 ] 95515438-102862434 | [ ] 88168442-95515438 | [ ] 80821445-88168441 | [ 3 ] 73474448-80821444 | [ ] 66127452-73474448 | [ ] 58780455-66127451 | [ 1 ] 51433458-58780454 | [ 1 ] 44086462-51433458 | [ 2 ] 36739465-44086461 | [ 3 ] 29392468-36739464 | [ 1 ] 22045472-29392468 | [ 4 ] 14698475-22045471 | [ 7 ] 7351478-14698474 | [ 5 ] 4482-7351478 |************************************************** [ 497 ] Storage Throughput = excellent ( 1037.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022690 bp ( 40020090 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:03 (hh:mm:ss) Elapsed Time Round Time: 00:22:08 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2309 repeats masked totaling 702435 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034900 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10034300 bp After Masking: 9180286 bp Masked: 8.51 % -- Input Database Coverage: 10034900 bp out of 1051698180 bp ( 0.95 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:09:38 (hh:mm:ss) Elapsed Time, 411 HSPs Collected Number of families returned by RECON: 196 Round Time: 00:10:35 (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 : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6888 repeats masked totaling 2257188 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027684 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30025684 bp After Masking: 27322600 bp Masked: 9.00 % -- Input Database Coverage: 40062584 bp out of 1051698180 bp ( 3.81 % ) Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:34:54 (hh:mm:ss) Elapsed Time, 4279 HSPs Collected Number of families returned by RECON: 1449 Round Time: 00:37:53 (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 : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21482 repeats masked totaling 6815455 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043877 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90039037 bp After Masking: 81781811 bp Masked: 9.17 % -- Input Database Coverage: 130106461 bp out of 1051698180 bp ( 12.37 % ) Sampling Time: 00:05:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 03:38:29 (hh:mm:ss) Elapsed Time, 38933 HSPs Collected Number of families returned by RECON: 9201 Round Time: 03:56:18 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76626 repeats masked totaling 23834252 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019433 bp Num Contigs Represented = 181 Non ambiguous bp: Initial: 270004033 bp After Masking: 242495259 bp Masked: 10.19 % -- Input Database Coverage: 400125894 bp out of 1051698180 bp ( 38.05 % ) Sampling Time: 00:19:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23225520 Comparison Time: 26:30:26 (hh:mm:ss) Elapsed Time, 176712 HSPs Collected Number of families returned by RECON: 62426 Round Time: 28:24:51 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatScout/RECON discovery complete: 356 families found Classification Time: 00:22:05 (hh:mm:ss) Elapsed Time Program Time: 33:53:50 (hh:mm:ss) Elapsed Time