RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JAN68a/RM_2193944.TueMar190312232024 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: 1710843143 Database = /dev/shm/rModeler.JAN68a/GCA_036250125.1_bDixPip1.hap1 - Sequences = 697 - Bases = 1165219370 - N50 = 75926125 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145631753-156033950 | [ 1 ] 135229556-145631752 | [ ] 124827360-135229556 | [ ] 114425163-124827359 | [ 2 ] 104022966-114425162 | [ ] 93620770-104022966 | [ ] 83218573-93620769 | [ ] 72816376-83218572 | [ 3 ] 62414180-72816376 | [ 2 ] 52011983-62414179 | [ ] 41609786-52011982 | [ ] 31207590-41609786 | [ 3 ] 20805393-31207589 | [ 5 ] 10403196-20805392 | [ 7 ] 1000-10403196 |************************************************** [ 674 ] Storage Throughput = good ( 829.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010244 bp ( 40008644 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:01 (hh:mm:ss) Elapsed Time Round Time: 00:28:44 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2968 repeats masked totaling 876770 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035949 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10035549 bp After Masking: 8894817 bp Masked: 11.37 % -- Input Database Coverage: 10035949 bp out of 1165219370 bp ( 0.86 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:34 (hh:mm:ss) Elapsed Time, 831 HSPs Collected Number of families returned by RECON: 296 Round Time: 00:07:50 (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 : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9075 repeats masked totaling 2847744 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014295 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30013095 bp After Masking: 26447022 bp Masked: 11.88 % -- Input Database Coverage: 40050244 bp out of 1165219370 bp ( 3.44 % ) Sampling Time: 00:03:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:34:20 (hh:mm:ss) Elapsed Time, 19882 HSPs Collected Number of families returned by RECON: 1569 Round Time: 00:37:47 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27163 repeats masked totaling 7988515 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018861 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 90014861 bp After Masking: 79289431 bp Masked: 11.92 % -- Input Database Coverage: 130069105 bp out of 1165219370 bp ( 11.16 % ) Sampling Time: 00:10:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 03:39:48 (hh:mm:ss) Elapsed Time, 53217 HSPs Collected Number of families returned by RECON: 9447 Round Time: 03:54:12 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92402 repeats masked totaling 29733792 bp(s). - TE Masking time 00:04:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033484 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 270018684 bp After Masking: 233650484 bp Masked: 13.47 % -- Input Database Coverage: 400102589 bp out of 1165219370 bp ( 34.34 % ) Sampling Time: 00:34:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 29:27:00 (hh:mm:ss) Elapsed Time, 281651 HSPs Collected Number of families returned by RECON: 60863 Round Time: 30:38:08 (hh:mm:ss) Elapsed Time : 322 families discovered. RepeatScout/RECON discovery complete: 550 families found Classification Time: 00:45:38 (hh:mm:ss) Elapsed Time Program Time: 36:32:19 (hh:mm:ss) Elapsed Time