RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rQ0U4Z/RM_386.SunMay142113362023 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: 1684124015 Database = /dev/shm/rModeler.rQ0U4Z/GCA_929443795.2_bAccGen1.2 - Sequences = 455 - Bases = 1398030142 - N50 = 37312042 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 83780511-89764762 | [ 1 ] 77796260-83780510 | [ ] 71812009-77796259 | [ ] 65827758-71812008 | [ ] 59843508-65827758 | [ ] 53859257-59843507 | [ 2 ] 47875006-53859256 | [ 2 ] 41890755-47875005 | [ 5 ] 35906504-41890754 | [ 4 ] 29922254-35906504 | [ 5 ] 23938003-29922253 | [ 7 ] 17953752-23938002 |* [ 9 ] 11969501-17953751 | [ 1 ] 5985250-11969500 | [ 2 ] 1000-5985250 |************************************************** [ 417 ] Storage Throughput = excellent ( 1219.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025795 bp ( 40024995 non ambiguous ) - Num Contigs Represented = 102 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:57 (hh:mm:ss) Elapsed Time Round Time: 00:29:34 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1230 repeats masked totaling 579843 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031724 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10031324 bp After Masking: 8726739 bp Masked: 13.01 % -- Input Database Coverage: 10031724 bp out of 1398030142 bp ( 0.72 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:18 (hh:mm:ss) Elapsed Time, 2849 HSPs Collected Number of families returned by RECON: 265 Round Time: 00:09:45 (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 : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4118 repeats masked totaling 2221691 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034142 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 30033742 bp After Masking: 25033272 bp Masked: 16.65 % -- Input Database Coverage: 40065866 bp out of 1398030142 bp ( 2.87 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:50:54 (hh:mm:ss) Elapsed Time, 23953 HSPs Collected Number of families returned by RECON: 1389 Round Time: 00:55:13 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13600 repeats masked totaling 6760384 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025263 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90023663 bp After Masking: 76642449 bp Masked: 14.86 % -- Input Database Coverage: 130091129 bp out of 1398030142 bp ( 9.31 % ) Sampling Time: 00:09:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 05:59:29 (hh:mm:ss) Elapsed Time, 334094 HSPs Collected Number of families returned by RECON: 8087 Round Time: 06:25:59 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53992 repeats masked totaling 23898964 bp(s). - TE Masking time 00:04:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033331 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 270026731 bp After Masking: 223989361 bp Masked: 17.05 % -- Input Database Coverage: 400124460 bp out of 1398030142 bp ( 28.62 % ) Sampling Time: 00:46:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 44:09:49 (hh:mm:ss) Elapsed Time, 3605634 HSPs Collected Number of families returned by RECON: 49453 Round Time: 45:45:02 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatScout/RECON discovery complete: 375 families found Classification Time: 00:37:12 (hh:mm:ss) Elapsed Time Program Time: 54:22:45 (hh:mm:ss) Elapsed Time