RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PEoN1a/RM_24330.SatNov252138332023 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: 1700977112 Database = /dev/shm/rModeler.PEoN1a/GCA_009859065.2_bTaeGut2.pri.v2 - Sequences = 541 - Bases = 1106297559 - N50 = 73512665 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 141463355-151567571 | [ 1 ] 131359140-141463355 | [ ] 121254924-131359139 | [ ] 111150709-121254924 | [ 2 ] 101046494-111150709 | [ ] 90942278-101046493 | [ ] 80838063-90942278 | [ ] 70733847-80838062 | [ 3 ] 60629632-70733847 | [ 1 ] 50525417-60629632 | [ ] 40421201-50525416 | [ ] 30316986-40421201 | [ 3 ] 20212770-30316985 | [ 4 ] 10108555-20212770 | [ 9 ] 4340-10108555 |************************************************** [ 518 ] Storage Throughput = excellent ( 1181.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40856388 bp ( 40006651 non ambiguous ) - Num Contigs Represented = 83 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:30 (hh:mm:ss) Elapsed Time Round Time: 00:26:31 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2642 repeats masked totaling 613776 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10224985 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10010496 bp After Masking: 9247567 bp Masked: 7.62 % -- Input Database Coverage: 10224985 bp out of 1106297559 bp ( 0.92 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:07:26 (hh:mm:ss) Elapsed Time, 672 HSPs Collected Number of families returned by RECON: 283 Round Time: 00:08:28 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7906 repeats masked totaling 2070929 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30671407 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30036159 bp After Masking: 27513823 bp Masked: 8.40 % -- Input Database Coverage: 40896392 bp out of 1106297559 bp ( 3.70 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:42:04 (hh:mm:ss) Elapsed Time, 6472 HSPs Collected Number of families returned by RECON: 1816 Round Time: 00:45:04 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25094 repeats masked totaling 6098461 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91605484 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 90039049 bp After Masking: 82534845 bp Masked: 8.33 % -- Input Database Coverage: 132501876 bp out of 1106297559 bp ( 11.98 % ) Sampling Time: 00:07:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2664586 Comparison Time: 05:13:57 (hh:mm:ss) Elapsed Time, 48194 HSPs Collected Number of families returned by RECON: 11305 Round Time: 05:25:29 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86134 repeats masked totaling 21683257 bp(s). - TE Masking time 00:04:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275026308 bp Num Contigs Represented = 252 Non ambiguous bp: Initial: 270038630 bp After Masking: 244259389 bp Masked: 9.55 % -- Input Database Coverage: 407528184 bp out of 1106297559 bp ( 36.84 % ) Sampling Time: 00:25:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24057516 Comparison Time: 42:53:57 (hh:mm:ss) Elapsed Time, 224219 HSPs Collected Number of families returned by RECON: 74890 Round Time: 44:49:17 (hh:mm:ss) Elapsed Time : 283 families discovered. RepeatScout/RECON discovery complete: 517 families found Classification Time: 01:11:49 (hh:mm:ss) Elapsed Time Program Time: 52:46:38 (hh:mm:ss) Elapsed Time