RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ZA2j4W/RM_1433921.MonNov180822532024 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: 1731946972 Database = /scratch/tmp/rModeler.ZA2j4W/GCA_023333525.1_rAspTig1.0.p - Sequences = 74 - Bases = 1335668279 Storage Throughput = excellent ( 1539.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007014 bp ( 40007014 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:45 (hh:mm:ss) Elapsed Time Round Time: 00:11:43 (hh:mm:ss) Elapsed Time : 629 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18250 repeats masked totaling 3299884 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002044 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10002044 bp After Masking: 6220064 bp Masked: 37.81 % -- Input Database Coverage: 10002044 bp out of 1335668279 bp ( 0.75 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 13749 HSPs Collected Number of families returned by RECON: 1501 Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59165 repeats masked totaling 10787569 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004966 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30004966 bp After Masking: 17921170 bp Masked: 40.27 % -- Input Database Coverage: 40007010 bp out of 1335668279 bp ( 3.00 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 49058 HSPs Collected Number of families returned by RECON: 4450 Round Time: 00:15:19 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191067 repeats masked totaling 34412096 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021358 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90021258 bp After Masking: 51719442 bp Masked: 42.55 % -- Input Database Coverage: 130028368 bp out of 1335668279 bp ( 9.74 % ) Sampling Time: 00:06:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:02:09 (hh:mm:ss) Elapsed Time, 218250 HSPs Collected Number of families returned by RECON: 13102 Round Time: 01:13:36 (hh:mm:ss) Elapsed Time : 438 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 642515 repeats masked totaling 116081522 bp(s). - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032616 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270031416 bp After Masking: 142634597 bp Masked: 47.18 % -- Input Database Coverage: 400060984 bp out of 1335668279 bp ( 29.95 % ) Sampling Time: 00:23:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 06:57:54 (hh:mm:ss) Elapsed Time, 486248 HSPs Collected Number of families returned by RECON: 41694 Round Time: 07:44:17 (hh:mm:ss) Elapsed Time : 995 families discovered. RepeatScout/RECON discovery complete: 2194 families found Classification Time: 00:31:20 (hh:mm:ss) Elapsed Time Program Time: 10:00:24 (hh:mm:ss) Elapsed Time