RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.S6518k/RM_2266306.TueJun251631002024 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: 1719358259 Database = /dev/shm/rModeler.S6518k/GCF_949316345.1_fPunPun2.1 - Sequences = 174 - Bases = 480434100 - N50 = 21811056 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33362094-35745030 | [ 2 ] 30979159-33362094 | [ ] 28596224-30979159 | [ 1 ] 26213288-28596223 | [ ] 23830353-26213288 | [ 2 ] 21447418-23830353 |* [ 4 ] 19064482-21447417 |* [ 6 ] 16681547-19064482 |* [ 5 ] 14298612-16681547 | [ 1 ] 11915676-14298611 | [ ] 9532741-11915676 | [ ] 7149806-9532741 | [ ] 4766870-7149805 | [ ] 2383935-4766870 | [ ] 1000-2383935 |************************************************** [ 153 ] Storage Throughput = excellent ( 1332.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013444 bp ( 40000847 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:24 (hh:mm:ss) Elapsed Time Round Time: 00:25:06 (hh:mm:ss) Elapsed Time : 310 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (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... 3504 repeats masked totaling 911375 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040226 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10036626 bp After Masking: 8410638 bp Masked: 16.20 % -- Input Database Coverage: 10040226 bp out of 480434100 bp ( 2.09 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:27 (hh:mm:ss) Elapsed Time, 4535 HSPs Collected Number of families returned by RECON: 1005 Round Time: 00:06:38 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10245 repeats masked totaling 2685492 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013089 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30004092 bp After Masking: 25095339 bp Masked: 16.36 % -- Input Database Coverage: 40053315 bp out of 480434100 bp ( 8.34 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:31:00 (hh:mm:ss) Elapsed Time, 31796 HSPs Collected Number of families returned by RECON: 4028 Round Time: 00:34:57 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35580 repeats masked totaling 8266158 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044545 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90016942 bp After Masking: 74519163 bp Masked: 17.22 % -- Input Database Coverage: 130097860 bp out of 480434100 bp ( 27.08 % ) Sampling Time: 00:10:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:49:22 (hh:mm:ss) Elapsed Time, 286722 HSPs Collected Number of families returned by RECON: 18165 Round Time: 04:10:54 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145685 repeats masked totaling 33090988 bp(s). - TE Masking time 00:06:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270116371 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 270034971 bp After Masking: 216436828 bp Masked: 19.85 % -- Input Database Coverage: 400214231 bp out of 480434100 bp ( 83.30 % ) Sampling Time: 00:31:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 28:09:35 (hh:mm:ss) Elapsed Time, 1257792 HSPs Collected Number of families returned by RECON: 76358 Round Time: 30:31:57 (hh:mm:ss) Elapsed Time : 712 families discovered. RepeatScout/RECON discovery complete: 1379 families found Classification Time: 01:20:12 (hh:mm:ss) Elapsed Time Program Time: 37:09:44 (hh:mm:ss) Elapsed Time