RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.PkYGTU/RM_2340311.WedDec40430242024 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: 1733315424 Database = /scratch/tmp/rModeler.PkYGTU/GCA_964263835.1_fCorLav1.hap2.1 - Sequences = 3980 - Bases = 2352365286 - N50 = 46350073 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 79874615-85579874 | [ 2 ] 74169357-79874615 | [ 1 ] 68464099-74169357 | [ 2 ] 62758840-68464098 | [ 1 ] 57053582-62758840 | [ 5 ] 51348324-57053582 | [ 3 ] 45643066-51348324 | [ 7 ] 39937807-45643065 | [ 7 ] 34232549-39937807 | [ 6 ] 28527291-34232549 | [ 3 ] 22822033-28527291 | [ 1 ] 17116774-22822032 | [ ] 11411516-17116774 | [ 2 ] 5706258-11411516 | [ ] 1000-5706258 |************************************************** [ 3940 ] Storage Throughput = excellent ( 1444.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041335 bp ( 40023735 non ambiguous ) - Num Contigs Represented = 269 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:11 (hh:mm:ss) Elapsed Time Round Time: 00:11:51 (hh:mm:ss) Elapsed Time : 970 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15191 repeats masked totaling 4550083 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039227 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 10035827 bp After Masking: 3795594 bp Masked: 62.18 % -- Input Database Coverage: 10039227 bp out of 2352365286 bp ( 0.43 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:02:34 (hh:mm:ss) Elapsed Time, 5716 HSPs Collected Number of families returned by RECON: 956 Round Time: 00:04:16 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48061 repeats masked totaling 14707437 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042179 bp Num Contigs Represented = 223 Non ambiguous bp: Initial: 30027979 bp After Masking: 11454513 bp Masked: 61.85 % -- Input Database Coverage: 40081406 bp out of 2352365286 bp ( 1.70 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 314028 Comparison Time: 00:10:25 (hh:mm:ss) Elapsed Time, 44045 HSPs Collected Number of families returned by RECON: 3290 Round Time: 00:14:37 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143850 repeats masked totaling 43252811 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044504 bp Num Contigs Represented = 503 Non ambiguous bp: Initial: 90005933 bp After Masking: 34691209 bp Masked: 61.46 % -- Input Database Coverage: 130125910 bp out of 2352365286 bp ( 5.53 % ) Sampling Time: 00:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2736630 Comparison Time: 00:52:29 (hh:mm:ss) Elapsed Time, 280198 HSPs Collected Number of families returned by RECON: 9702 Round Time: 01:09:51 (hh:mm:ss) Elapsed Time : 479 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 492386 repeats masked totaling 143923218 bp(s). - TE Masking time 00:04:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270117631 bp Num Contigs Represented = 1088 Non ambiguous bp: Initial: 270010409 bp After Masking: 90866760 bp Masked: 66.35 % -- Input Database Coverage: 400243541 bp out of 2352365286 bp ( 17.01 % ) Sampling Time: 00:41:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24728028 Comparison Time: 05:06:07 (hh:mm:ss) Elapsed Time, 812634 HSPs Collected Number of families returned by RECON: 30137 Round Time: 06:04:59 (hh:mm:ss) Elapsed Time : 1054 families discovered. RepeatScout/RECON discovery complete: 2584 families found Classification Time: 00:56:08 (hh:mm:ss) Elapsed Time Program Time: 08:41:42 (hh:mm:ss) Elapsed Time