RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cBfVKq/RM_1790539.ThuApr101845012025 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: 1744335899 Database = /dev/shm/rModeler.cBfVKq/GCF_964237555.1_mOryCun1.1 - Sequences = 221 - Bases = 2804657419 - N50 = 164456403 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 222327774-238208258 | [ 1 ] 206447290-222327773 | [ ] 190566806-206447289 | [ 1 ] 174686322-190566805 | [ 2 ] 158805838-174686321 | [ 3 ] 142925354-158805837 | [ 1 ] 127044870-142925353 | [ 2 ] 111164387-127044870 | [ 3 ] 95283903-111164386 | [ 2 ] 79403419-95283902 | [ 1 ] 63522935-79403418 |* [ 4 ] 47642451-63522934 | [ 1 ] 31761967-47642450 | [ 1 ] 15881483-31761966 | [ ] 1000-15881483 |************************************************** [ 199 ] Storage Throughput = excellent ( 1794.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009468 bp ( 40003668 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:45 (hh:mm:ss) Elapsed Time Round Time: 00:11:46 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15150 repeats masked totaling 3664330 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031192 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10028592 bp After Masking: 6131496 bp Masked: 38.86 % -- Input Database Coverage: 10031192 bp out of 2804657419 bp ( 0.36 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 5522 HSPs Collected Number of families returned by RECON: 575 Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47443 repeats masked totaling 11292181 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018119 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30014919 bp After Masking: 18244542 bp Masked: 39.22 % -- Input Database Coverage: 40049311 bp out of 2804657419 bp ( 1.43 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:08 (hh:mm:ss) Elapsed Time, 19724 HSPs Collected Number of families returned by RECON: 1856 Round Time: 00:14:21 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149032 repeats masked totaling 34605035 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037173 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90021373 bp After Masking: 53853014 bp Masked: 40.18 % -- Input Database Coverage: 130086484 bp out of 2804657419 bp ( 4.64 % ) Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:07:00 (hh:mm:ss) Elapsed Time, 78562 HSPs Collected Number of families returned by RECON: 6975 Round Time: 01:14:30 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 486710 repeats masked totaling 111326991 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270072686 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270027886 bp After Masking: 153295553 bp Masked: 43.23 % -- Input Database Coverage: 400159170 bp out of 2804657419 bp ( 14.27 % ) Sampling Time: 00:18:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 07:41:19 (hh:mm:ss) Elapsed Time, 318720 HSPs Collected Number of families returned by RECON: 27783 Round Time: 08:06:37 (hh:mm:ss) Elapsed Time : 347 families discovered. RepeatScout/RECON discovery complete: 722 families found Classification Time: 00:16:00 (hh:mm:ss) Elapsed Time Program Time: 10:07:04 (hh:mm:ss) Elapsed Time