RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Fiu1fk/RM_14415.SunMay71030432023 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: 1683480640 Database = /dev/shm/rModeler.Fiu1fk/GCA_026419985.1_mKogBre1_haplotype_2 - Sequences = 391 - Bases = 2613416393 - N50 = 135682998 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 189685260-203233528 | [ 3 ] 176136992-189685259 | [ 1 ] 162588725-176136992 | [ ] 149040457-162588724 | [ 1 ] 135492190-149040457 | [ 2 ] 121943922-135492189 | [ ] 108395654-121943921 | [ 3 ] 94847387-108395654 | [ 3 ] 81299119-94847386 | [ 4 ] 67750852-81299119 | [ 1 ] 54202584-67750851 | [ 3 ] 40654316-54202583 | [ ] 27106049-40654316 | [ ] 13557781-27106048 | [ ] 9514-13557781 |************************************************** [ 370 ] Storage Throughput = excellent ( 1143.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023803 bp ( 40021573 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:48 (hh:mm:ss) Elapsed Time Round Time: 00:40:19 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12477 repeats masked totaling 3178628 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006008 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10005995 bp After Masking: 6663207 bp Masked: 33.41 % -- Input Database Coverage: 10006008 bp out of 2613416393 bp ( 0.38 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:10:15 (hh:mm:ss) Elapsed Time, 40987 HSPs Collected Number of families returned by RECON: 749 Round Time: 00:12:41 (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 : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40798 repeats masked totaling 10277352 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017792 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30015575 bp After Masking: 19227743 bp Masked: 35.94 % -- Input Database Coverage: 40023800 bp out of 2613416393 bp ( 1.53 % ) Sampling Time: 00:03:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:43:41 (hh:mm:ss) Elapsed Time, 31447 HSPs Collected Number of families returned by RECON: 2179 Round Time: 00:48:28 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131905 repeats masked totaling 32629940 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018958 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90017039 bp After Masking: 55570819 bp Masked: 38.27 % -- Input Database Coverage: 130042758 bp out of 2613416393 bp ( 4.98 % ) Sampling Time: 00:11:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:48:08 (hh:mm:ss) Elapsed Time, 202077 HSPs Collected Number of families returned by RECON: 8328 Round Time: 04:06:23 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 451205 repeats masked totaling 107696223 bp(s). - TE Masking time 00:07:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270072903 bp Num Contigs Represented = 171 Non ambiguous bp: Initial: 270016597 bp After Masking: 157919233 bp Masked: 41.51 % -- Input Database Coverage: 400115661 bp out of 2613416393 bp ( 15.31 % ) Sampling Time: 00:36:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 25:43:51 (hh:mm:ss) Elapsed Time, 1197524 HSPs Collected Number of families returned by RECON: 29940 Round Time: 26:44:47 (hh:mm:ss) Elapsed Time : 330 families discovered. RepeatScout/RECON discovery complete: 772 families found Classification Time: 00:35:54 (hh:mm:ss) Elapsed Time Program Time: 33:08:32 (hh:mm:ss) Elapsed Time