RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.V2TfKU/RM_173394.WedJul170136472024 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: 1721205399 Database = /dev/shm/rModeler.V2TfKU/GCF_024500275.1_UOR_Pequ_1.1 - Sequences = 1537 - Bases = 666479602 - N50 = 30068750 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48178710-51620032 | [ 1 ] 44737389-48178710 | [ 1 ] 41296068-44737389 | [ ] 37854747-41296068 | [ ] 34413426-37854747 | [ ] 30972105-34413426 | [ 6 ] 27530784-30972105 | [ 3 ] 24089462-27530783 | [ 4 ] 20648141-24089462 | [ 2 ] 17206820-20648141 | [ 2 ] 13765499-17206820 | [ 2 ] 10324178-13765499 | [ 1 ] 6882857-10324178 | [ 1 ] 3441536-6882857 | [ ] 215-3441536 |************************************************** [ 1514 ] Storage Throughput = good ( 731.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009047 bp ( 40009047 non ambiguous ) - Num Contigs Represented = 140 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:22 (hh:mm:ss) Elapsed Time Round Time: 00:35:14 (hh:mm:ss) Elapsed Time : 812 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18311 repeats masked totaling 3324526 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027515 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10027515 bp After Masking: 6337854 bp Masked: 36.80 % -- Input Database Coverage: 10027515 bp out of 666479602 bp ( 1.50 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34980 Comparison Time: 00:37:00 (hh:mm:ss) Elapsed Time, 15699 HSPs Collected Number of families returned by RECON: 1915 Round Time: 00:39:51 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54449 repeats masked totaling 9705517 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021466 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 30021466 bp After Masking: 18171788 bp Masked: 39.47 % -- Input Database Coverage: 40048981 bp out of 666479602 bp ( 6.01 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 322003 Comparison Time: 02:03:32 (hh:mm:ss) Elapsed Time, 73430 HSPs Collected Number of families returned by RECON: 5312 Round Time: 02:13:46 (hh:mm:ss) Elapsed Time : 184 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 182101 repeats masked totaling 32803523 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030079 bp Num Contigs Represented = 302 Non ambiguous bp: Initial: 90029779 bp After Masking: 51303508 bp Masked: 43.01 % -- Input Database Coverage: 130079060 bp out of 666479602 bp ( 19.52 % ) Sampling Time: 00:10:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2888406 Comparison Time: 06:54:52 (hh:mm:ss) Elapsed Time, 294348 HSPs Collected Number of families returned by RECON: 15282 Round Time: 07:24:13 (hh:mm:ss) Elapsed Time : 568 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 646942 repeats masked totaling 114068291 bp(s). - TE Masking time 00:09:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019917 bp Num Contigs Represented = 734 Non ambiguous bp: Initial: 270019097 bp After Masking: 138311822 bp Masked: 48.78 % -- Input Database Coverage: 400098977 bp out of 666479602 bp ( 60.03 % ) Sampling Time: 00:32:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26038936 Comparison Time: 39:40:20 (hh:mm:ss) Elapsed Time, 543443 HSPs Collected Number of families returned by RECON: 45518 Round Time: 41:10:17 (hh:mm:ss) Elapsed Time : 1033 families discovered. RepeatScout/RECON discovery complete: 2627 families found Classification Time: 01:08:24 (hh:mm:ss) Elapsed Time Program Time: 53:11:45 (hh:mm:ss) Elapsed Time