RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.l17jMh/RM_2161.MonDec40539252023 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: 1701697165 Database = /dev/shm/rModeler.l17jMh/GCA_030936125.1_bGavSte3.hap1 - Sequences = 2965 - Bases = 1403461371 - N50 = 63071665 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124528402-133422388 | [ 1 ] 115634416-124528401 | [ ] 106740431-115634416 | [ 1 ] 97846445-106740430 | [ 1 ] 88952460-97846445 | [ 1 ] 80058474-88952459 | [ 1 ] 71164488-80058473 | [ ] 62270503-71164488 | [ 2 ] 53376517-62270502 | [ ] 44482532-53376517 | [ 2 ] 35588546-44482531 | [ 2 ] 26694560-35588545 | [ 1 ] 17800575-26694560 | [ 9 ] 8906589-17800574 | [ 8 ] 12604-8906589 |************************************************** [ 2936 ] Storage Throughput = excellent ( 1133.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028084 bp ( 40025884 non ambiguous ) - Num Contigs Represented = 178 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:04 (hh:mm:ss) Elapsed Time Round Time: 00:37:25 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (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... 1376 repeats masked totaling 550186 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013074 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10012674 bp After Masking: 8526049 bp Masked: 14.85 % -- Input Database Coverage: 10013074 bp out of 1403461371 bp ( 0.71 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:42 (hh:mm:ss) Elapsed Time, 770 HSPs Collected Number of families returned by RECON: 212 Round Time: 00:08:18 (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 : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4628 repeats masked totaling 1820543 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015006 bp Num Contigs Represented = 142 Non ambiguous bp: Initial: 30013206 bp After Masking: 25533505 bp Masked: 14.93 % -- Input Database Coverage: 40028080 bp out of 1403461371 bp ( 2.85 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 304590 Comparison Time: 00:33:32 (hh:mm:ss) Elapsed Time, 7300 HSPs Collected Number of families returned by RECON: 1416 Round Time: 00:38:17 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15619 repeats masked totaling 5789330 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038350 bp Num Contigs Represented = 375 Non ambiguous bp: Initial: 90034950 bp After Masking: 75808871 bp Masked: 15.80 % -- Input Database Coverage: 130066430 bp out of 1403461371 bp ( 9.27 % ) Sampling Time: 00:11:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2720278 Comparison Time: 04:05:00 (hh:mm:ss) Elapsed Time, 73971 HSPs Collected Number of families returned by RECON: 7270 Round Time: 04:37:30 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61973 repeats masked totaling 23362502 bp(s). - TE Masking time 00:05:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044810 bp Num Contigs Represented = 929 Non ambiguous bp: Initial: 270034810 bp After Masking: 220130219 bp Masked: 18.48 % -- Input Database Coverage: 400111240 bp out of 1403461371 bp ( 28.51 % ) Sampling Time: 00:43:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24601605 Comparison Time: 32:43:29 (hh:mm:ss) Elapsed Time, 217185 HSPs Collected Number of families returned by RECON: 43140 Round Time: 34:40:51 (hh:mm:ss) Elapsed Time : 226 families discovered. RepeatScout/RECON discovery complete: 384 families found Classification Time: 01:06:35 (hh:mm:ss) Elapsed Time Program Time: 41:48:56 (hh:mm:ss) Elapsed Time