RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.14d6DP/RM_31331.TueJul90248222024 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: 1720518501 Database = /dev/shm/rModeler.14d6DP/GCF_001640805.2_TLL_Latcal_v3 - Sequences = 2997 - Bases = 673814222 - N50 = 25703306 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 28725328-30776907 | [ 3 ] 26673750-28725328 | [ 6 ] 24622172-26673750 | [ 4 ] 22570593-24622171 | [ 6 ] 20519015-22570593 | [ ] 18467437-20519015 | [ 2 ] 16415858-18467436 | [ 1 ] 14364280-16415858 | [ ] 12312702-14364280 | [ 2 ] 10261123-12312701 | [ ] 8209545-10261123 | [ ] 6157967-8209545 | [ ] 4106388-6157966 | [ ] 2054810-4106388 | [ ] 3232-2054810 |************************************************** [ 2973 ] Storage Throughput = excellent ( 1019.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40456914 bp ( 40027563 non ambiguous ) - Num Contigs Represented = 243 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:42 (hh:mm:ss) Elapsed Time Round Time: 00:28:58 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5973 repeats masked totaling 810537 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10207422 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 10032711 bp After Masking: 8996777 bp Masked: 10.33 % -- Input Database Coverage: 10207422 bp out of 673814222 bp ( 1.51 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 39903 Comparison Time: 00:07:36 (hh:mm:ss) Elapsed Time, 9103 HSPs Collected Number of families returned by RECON: 1614 Round Time: 00:08:42 (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 : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19950 repeats masked totaling 2710000 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30265568 bp Num Contigs Represented = 179 Non ambiguous bp: Initial: 30010928 bp After Masking: 26616121 bp Masked: 11.31 % -- Input Database Coverage: 40472990 bp out of 673814222 bp ( 6.01 % ) Sampling Time: 00:02:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 333336 Comparison Time: 00:41:29 (hh:mm:ss) Elapsed Time, 46438 HSPs Collected Number of families returned by RECON: 6113 Round Time: 00:46:01 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66241 repeats masked totaling 8941440 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91283288 bp Num Contigs Represented = 434 Non ambiguous bp: Initial: 90033627 bp After Masking: 78808276 bp Masked: 12.47 % -- Input Database Coverage: 131756278 bp out of 673814222 bp ( 19.55 % ) Sampling Time: 00:08:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3039345 Comparison Time: 05:04:19 (hh:mm:ss) Elapsed Time, 278422 HSPs Collected Number of families returned by RECON: 23852 Round Time: 05:32:06 (hh:mm:ss) Elapsed Time : 375 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 266612 repeats masked totaling 39039942 bp(s). - TE Masking time 00:09:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272825030 bp Num Contigs Represented = 1311 Non ambiguous bp: Initial: 270008798 bp After Masking: 223667605 bp Masked: 17.16 % -- Input Database Coverage: 404581308 bp out of 673814222 bp ( 60.04 % ) Sampling Time: 00:29:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27613596 Comparison Time: 37:09:05 (hh:mm:ss) Elapsed Time, 897159 HSPs Collected Number of families returned by RECON: 89946 Round Time: 40:51:25 (hh:mm:ss) Elapsed Time : 985 families discovered. RepeatScout/RECON discovery complete: 1785 families found Classification Time: 02:04:10 (hh:mm:ss) Elapsed Time Program Time: 49:51:22 (hh:mm:ss) Elapsed Time