RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Bhak8k/RM_1595969.ThuJul110741502024 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: 1720708909 Database = /dev/shm/rModeler.Bhak8k/GCF_027789165.1_UI_Nfuz_MZM_1.0 - Sequences = 2681 - Bases = 1513041927 - N50 = 42477515 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 88673119-95006899 | [ 1 ] 82339339-88673118 | [ ] 76005559-82339338 | [ 1 ] 69671779-76005558 | [ 2 ] 63337999-69671778 | [ 1 ] 57004219-63337998 | [ 2 ] 50670439-57004218 | [ 2 ] 44336659-50670438 | [ 2 ] 38002879-44336658 | [ 4 ] 31669099-38002878 | [ 3 ] 25335319-31669098 | [ ] 19001539-25335318 | [ 1 ] 12667759-19001538 | [ 1 ] 6333979-12667758 | [ 13 ] 200-6333979 |************************************************** [ 2648 ] Storage Throughput = excellent ( 1424.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42817344 bp ( 40031663 non ambiguous ) - Num Contigs Represented = 260 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:21 (hh:mm:ss) Elapsed Time Round Time: 00:38:01 (hh:mm:ss) Elapsed Time : 720 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10360 repeats masked totaling 3194258 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10526797 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 10006200 bp After Masking: 4089965 bp Masked: 59.13 % -- Input Database Coverage: 10526797 bp out of 1513041927 bp ( 0.70 % ) Sampling Time: 00:03:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 50643 HSPs Collected Number of families returned by RECON: 721 Round Time: 00:09:26 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32935 repeats masked totaling 10392083 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32290484 bp Num Contigs Represented = 214 Non ambiguous bp: Initial: 30025400 bp After Masking: 12597874 bp Masked: 58.04 % -- Input Database Coverage: 42817281 bp out of 1513041927 bp ( 2.83 % ) Sampling Time: 00:11:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 369370 Comparison Time: 00:26:02 (hh:mm:ss) Elapsed Time, 271184 HSPs Collected Number of families returned by RECON: 2635 Round Time: 00:39:18 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105774 repeats masked totaling 33293140 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96811546 bp Num Contigs Represented = 434 Non ambiguous bp: Initial: 90011645 bp After Masking: 34467616 bp Masked: 61.71 % -- Input Database Coverage: 139628827 bp out of 1513041927 bp ( 9.23 % ) Sampling Time: 00:35:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3237240 Comparison Time: 02:52:41 (hh:mm:ss) Elapsed Time, 304304 HSPs Collected Number of families returned by RECON: 7361 Round Time: 03:40:20 (hh:mm:ss) Elapsed Time : 367 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 357902 repeats masked totaling 111048138 bp(s). - TE Masking time 00:08:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 289744678 bp Num Contigs Represented = 934 Non ambiguous bp: Initial: 270006037 bp After Masking: 91196782 bp Masked: 66.22 % -- Input Database Coverage: 429373505 bp out of 1513041927 bp ( 28.38 % ) Sampling Time: 01:26:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29180980 Comparison Time: 11:30:52 (hh:mm:ss) Elapsed Time, 683047 HSPs Collected Number of families returned by RECON: 22117 Round Time: 13:23:50 (hh:mm:ss) Elapsed Time : 870 families discovered. RepeatScout/RECON discovery complete: 2031 families found Classification Time: 01:42:14 (hh:mm:ss) Elapsed Time Program Time: 20:13:09 (hh:mm:ss) Elapsed Time