RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9yZCrr/RM_277915.FriJul50000232024 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: 1720162822 Database = /dev/shm/rModeler.9yZCrr/GCF_036321145.1_Pm_UMD_F - Sequences = 792 - Bases = 940981472 - N50 = 44633640 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 88447992-94765109 | [ 1 ] 82130875-88447991 | [ ] 75813758-82130874 | [ ] 69496641-75813757 | [ 2 ] 63179525-69496641 | [ 1 ] 56862408-63179524 | [ ] 50545291-56862407 | [ 1 ] 44228174-50545290 | [ 2 ] 37911057-44228173 | [ 8 ] 31593941-37911057 | [ 4 ] 25276824-31593940 | [ ] 18959707-25276823 | [ ] 12642590-18959706 | [ ] 6325473-12642589 | [ ] 8357-6325473 |************************************************** [ 773 ] Storage Throughput = good ( 999.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022860 bp ( 40022860 non ambiguous ) - Num Contigs Represented = 66 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:58 (hh:mm:ss) Elapsed Time Round Time: 00:25:08 (hh:mm:ss) Elapsed Time : 686 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 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10341 repeats masked totaling 2440973 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012603 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10012603 bp After Masking: 7139511 bp Masked: 28.69 % -- Input Database Coverage: 10012603 bp out of 940981472 bp ( 1.06 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:28 (hh:mm:ss) Elapsed Time, 6356 HSPs Collected Number of families returned by RECON: 1233 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32658 repeats masked totaling 8008851 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010254 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30010254 bp After Masking: 21243270 bp Masked: 29.21 % -- Input Database Coverage: 40022857 bp out of 940981472 bp ( 4.25 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:29:19 (hh:mm:ss) Elapsed Time, 41647 HSPs Collected Number of families returned by RECON: 4243 Round Time: 00:34:26 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106276 repeats masked totaling 24369657 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011582 bp Num Contigs Represented = 109 Non ambiguous bp: Initial: 90011432 bp After Masking: 63124494 bp Masked: 29.87 % -- Input Database Coverage: 130034439 bp out of 940981472 bp ( 13.82 % ) Sampling Time: 00:10:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 03:04:37 (hh:mm:ss) Elapsed Time, 248857 HSPs Collected Number of families returned by RECON: 14489 Round Time: 03:25:02 (hh:mm:ss) Elapsed Time : 428 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 375290 repeats masked totaling 88019769 bp(s). - TE Masking time 00:11:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015273 bp Num Contigs Represented = 294 Non ambiguous bp: Initial: 270014973 bp After Masking: 174247950 bp Masked: 35.47 % -- Input Database Coverage: 400049712 bp out of 940981472 bp ( 42.51 % ) Sampling Time: 00:34:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23403061 Comparison Time: 20:19:55 (hh:mm:ss) Elapsed Time, 796361 HSPs Collected Number of families returned by RECON: 51241 Round Time: 22:17:24 (hh:mm:ss) Elapsed Time : 1165 families discovered. RepeatScout/RECON discovery complete: 2391 families found Classification Time: 02:03:36 (hh:mm:ss) Elapsed Time Program Time: 28:53:20 (hh:mm:ss) Elapsed Time