RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LPLGpN/RM_70237.TueJan32101472023 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: 1672808507 Database = /dev/shm/rModeler.LPLGpN/GCA_014839755.1_bSylBor1.pri - Sequences = 176 - Bases = 1045652180 - N50 = 86481582 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142937003-153146699 | [ 1 ] 132727307-142937002 | [ ] 122517612-132727307 | [ ] 112307916-122517611 | [ 2 ] 102098221-112307916 | [ ] 91888525-102098220 | [ ] 81678829-91888524 | [ 1 ] 71469134-81678829 | [ 2 ] 61259438-71469133 | [ 1 ] 51049743-61259438 | [ ] 40840047-51049742 | [ ] 30630351-40840046 | [ 3 ] 20420656-30630351 | [ 3 ] 10210960-20420655 |** [ 8 ] 1265-10210960 |************************************************** [ 155 ] Storage Throughput = good ( 986.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40228421 bp ( 40030343 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:23 (hh:mm:ss) Elapsed Time Round Time: 00:23:49 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2868 repeats masked totaling 536153 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10078817 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10038817 bp After Masking: 9367204 bp Masked: 6.69 % -- Input Database Coverage: 10078817 bp out of 1045652180 bp ( 0.96 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:06 (hh:mm:ss) Elapsed Time, 926 HSPs Collected Number of families returned by RECON: 310 Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8802 repeats masked totaling 1751159 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30189604 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30031526 bp After Masking: 27767999 bp Masked: 7.54 % -- Input Database Coverage: 40268421 bp out of 1045652180 bp ( 3.85 % ) Sampling Time: 00:03:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:38:24 (hh:mm:ss) Elapsed Time, 7619 HSPs Collected Number of families returned by RECON: 1786 Round Time: 00:41:55 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26291 repeats masked totaling 4933417 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90104458 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90018629 bp After Masking: 83480875 bp Masked: 7.26 % -- Input Database Coverage: 130372879 bp out of 1045652180 bp ( 12.47 % ) Sampling Time: 00:09:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 04:25:12 (hh:mm:ss) Elapsed Time, 44897 HSPs Collected Number of families returned by RECON: 12082 Round Time: 04:37:01 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84550 repeats masked totaling 16894640 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270617111 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 270025858 bp After Masking: 248460734 bp Masked: 7.99 % -- Input Database Coverage: 400989990 bp out of 1045652180 bp ( 38.35 % ) Sampling Time: 00:26:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 35:21:10 (hh:mm:ss) Elapsed Time, 249360 HSPs Collected Number of families returned by RECON: 80795 Round Time: 37:26:33 (hh:mm:ss) Elapsed Time : 241 families discovered. RepeatScout/RECON discovery complete: 425 families found Classification Time: 00:31:24 (hh:mm:ss) Elapsed Time Program Time: 43:49:02 (hh:mm:ss) Elapsed Time