RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.uMy7Af/RM_3028970.WedApr160520502025 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: 1744806047 Database = /data/tmp/rModeler.uMy7Af/GCA_023637945.2_bPhaSup1.pri - Sequences = 65 - Bases = 1020009783 Storage Throughput = excellent ( 1563.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40257438 bp ( 40039248 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:33 (hh:mm:ss) Elapsed Time Round Time: 00:13:33 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2504 repeats masked totaling 596153 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10129251 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10031688 bp After Masking: 9336009 bp Masked: 6.93 % -- Input Database Coverage: 10129251 bp out of 1020009783 bp ( 0.99 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 441 HSPs Collected Number of families returned by RECON: 272 Round Time: 00:06:06 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7693 repeats masked totaling 1860155 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30128156 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30007529 bp After Masking: 27874625 bp Masked: 7.11 % -- Input Database Coverage: 40257407 bp out of 1020009783 bp ( 3.95 % ) Sampling Time: 00:01:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:30:30 (hh:mm:ss) Elapsed Time, 4411 HSPs Collected Number of families returned by RECON: 1858 Round Time: 00:32:24 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:05 (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... 22192 repeats masked totaling 5365571 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90467438 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90027267 bp After Masking: 83974203 bp Masked: 6.72 % -- Input Database Coverage: 130724845 bp out of 1020009783 bp ( 12.82 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:45:05 (hh:mm:ss) Elapsed Time, 37690 HSPs Collected Number of families returned by RECON: 12102 Round Time: 02:51:26 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75924 repeats masked totaling 18153327 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271008601 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 270001289 bp After Masking: 249564962 bp Masked: 7.57 % -- Input Database Coverage: 401733446 bp out of 1020009783 bp ( 39.39 % ) Sampling Time: 00:15:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 21:24:03 (hh:mm:ss) Elapsed Time, 194058 HSPs Collected Number of families returned by RECON: 80353 Round Time: 22:07:47 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatScout/RECON discovery complete: 283 families found Classification Time: 00:08:42 (hh:mm:ss) Elapsed Time Program Time: 25:59:58 (hh:mm:ss) Elapsed Time