RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MgwE5Y/RM_23421.SatJun292016262024 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: 1719717383 Database = /dev/shm/rModeler.MgwE5Y/GCA_014183145.1_ASM1418314v1 - Sequences = 34462 - Bases = 684633790 - N50 = 27114551 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30334623-32501368 | [ 2 ] 28167878-30334622 | [ 4 ] 26001134-28167878 | [ 5 ] 23834389-26001133 | [ 4 ] 21667645-23834389 | [ 5 ] 19500900-21667644 | [ 1 ] 17334156-19500900 | [ 2 ] 15167411-17334155 | [ ] 13000667-15167411 | [ 1 ] 10833922-13000666 | [ ] 8667178-10833922 | [ ] 6500433-8667177 | [ ] 4333689-6500433 | [ ] 2166944-4333688 | [ 6 ] 200-2166944 |************************************************** [ 34432 ] Storage Throughput = excellent ( 1032.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41736918 bp ( 40019900 non ambiguous ) - Num Contigs Represented = 2169 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:54 (hh:mm:ss) Elapsed Time Round Time: 00:24:07 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6474 repeats masked totaling 811259 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10480680 bp Num Contigs Represented = 500 Non ambiguous bp: Initial: 10031214 bp After Masking: 9067691 bp Masked: 9.61 % -- Input Database Coverage: 10480680 bp out of 684633790 bp ( 1.53 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 254541 Comparison Time: 00:08:20 (hh:mm:ss) Elapsed Time, 9043 HSPs Collected Number of families returned by RECON: 1789 Round Time: 00:09:19 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22211 repeats masked totaling 2881678 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31296621 bp Num Contigs Represented = 1696 Non ambiguous bp: Initial: 30029069 bp After Masking: 26717100 bp Masked: 11.03 % -- Input Database Coverage: 41777301 bp out of 684633790 bp ( 6.10 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2828631 Comparison Time: 00:43:34 (hh:mm:ss) Elapsed Time, 53005 HSPs Collected Number of families returned by RECON: 6601 Round Time: 00:47:22 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79325 repeats masked totaling 10604847 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94145891 bp Num Contigs Represented = 4623 Non ambiguous bp: Initial: 90020603 bp After Masking: 78189844 bp Masked: 13.14 % -- Input Database Coverage: 135923192 bp out of 684633790 bp ( 19.85 % ) Sampling Time: 00:05:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22744140 Comparison Time: 04:58:52 (hh:mm:ss) Elapsed Time, 302988 HSPs Collected Number of families returned by RECON: 24724 Round Time: 05:26:12 (hh:mm:ss) Elapsed Time : 462 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 307998 repeats masked totaling 44544097 bp(s). - TE Masking time 00:08:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 282772373 bp Num Contigs Represented = 14294 Non ambiguous bp: Initial: 270009957 bp After Masking: 221648651 bp Masked: 17.91 % -- Input Database Coverage: 418695565 bp out of 684633790 bp ( 61.16 % ) Sampling Time: 00:21:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 214296753 Comparison Time: 38:08:46 (hh:mm:ss) Elapsed Time, 905469 HSPs Collected Number of families returned by RECON: 90507 Round Time: 41:52:44 (hh:mm:ss) Elapsed Time : 1132 families discovered. RepeatScout/RECON discovery complete: 2019 families found Classification Time: 01:33:53 (hh:mm:ss) Elapsed Time Program Time: 50:13:37 (hh:mm:ss) Elapsed Time