RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.PqoXG8/RM_3051034.MonDec91041532024 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: 1733769713 Database = /scratch/tmp/rModeler.PqoXG8/GCA_040955645.1_LycPic1.final.hap1 - Sequences = 85 - Bases = 2260356192 Storage Throughput = excellent ( 1509.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007921 bp ( 40007921 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:16 (hh:mm:ss) Elapsed Time Round Time: 00:11:40 (hh:mm:ss) Elapsed Time : 179 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 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13232 repeats masked totaling 2422745 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003767 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10003767 bp After Masking: 7474083 bp Masked: 25.29 % -- Input Database Coverage: 10003767 bp out of 2260356192 bp ( 0.44 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 6238 HSPs Collected Number of families returned by RECON: 838 Round Time: 00:03:37 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43047 repeats masked totaling 7580349 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004153 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30004153 bp After Masking: 22074903 bp Masked: 26.43 % -- Input Database Coverage: 40007920 bp out of 2260356192 bp ( 1.77 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:34 (hh:mm:ss) Elapsed Time, 27854 HSPs Collected Number of families returned by RECON: 2683 Round Time: 00:15:35 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139675 repeats masked totaling 25892368 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018441 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90018141 bp After Masking: 63043728 bp Masked: 29.97 % -- Input Database Coverage: 130026361 bp out of 2260356192 bp ( 5.75 % ) Sampling Time: 00:04:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:19:18 (hh:mm:ss) Elapsed Time, 64421 HSPs Collected Number of families returned by RECON: 9148 Round Time: 01:25:23 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459641 repeats masked totaling 84727633 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008845 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270007445 bp After Masking: 182471482 bp Masked: 32.42 % -- Input Database Coverage: 400035206 bp out of 2260356192 bp ( 17.70 % ) Sampling Time: 00:13:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 09:20:40 (hh:mm:ss) Elapsed Time, 185183 HSPs Collected Number of families returned by RECON: 40731 Round Time: 09:47:47 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 755 families found Classification Time: 00:13:43 (hh:mm:ss) Elapsed Time Program Time: 11:57:45 (hh:mm:ss) Elapsed Time