RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JDByzX/RM_218279.WedJan41651142023 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: 1672879873 Database = /dev/shm/rModeler.JDByzX/GCA_016904835.1_bAcaChl1.pri - Sequences = 206 - Bases = 1077387582 - N50 = 46605043 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127469060-136573486 | [ 1 ] 118364635-127469060 | [ ] 109260210-118364635 | [ ] 100155784-109260209 | [ ] 91051359-100155784 | [ 1 ] 81946934-91051359 | [ ] 72842508-81946933 | [ 1 ] 63738083-72842508 | [ ] 54633658-63738083 | [ 1 ] 45529232-54633657 | [ 3 ] 36424807-45529232 | [ 2 ] 27320382-36424807 | [ 3 ] 18215956-27320381 |** [ 9 ] 9111531-18215956 |* [ 7 ] 7106-9111531 |************************************************** [ 178 ] Storage Throughput = excellent ( 1656.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40205293 bp ( 40023155 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:28 (hh:mm:ss) Elapsed Time Round Time: 00:14:41 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3304 repeats masked totaling 799489 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10059206 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10018602 bp After Masking: 9090551 bp Masked: 9.26 % -- Input Database Coverage: 10059206 bp out of 1077387582 bp ( 0.93 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 607 HSPs Collected Number of families returned by RECON: 272 Round Time: 00:06:41 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10942 repeats masked totaling 2667785 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30146007 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30004473 bp After Masking: 26900434 bp Masked: 10.35 % -- Input Database Coverage: 40205213 bp out of 1077387582 bp ( 3.73 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:16 (hh:mm:ss) Elapsed Time, 5575 HSPs Collected Number of families returned by RECON: 1548 Round Time: 00:28:15 (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 : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31066 repeats masked totaling 7700463 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90373867 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90011442 bp After Masking: 81058078 bp Masked: 9.95 % -- Input Database Coverage: 130579080 bp out of 1077387582 bp ( 12.12 % ) Sampling Time: 00:06:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:46:50 (hh:mm:ss) Elapsed Time, 50290 HSPs Collected Number of families returned by RECON: 10778 Round Time: 02:54:36 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101591 repeats masked totaling 24854193 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271149393 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 270030962 bp After Masking: 241146151 bp Masked: 10.70 % -- Input Database Coverage: 401728473 bp out of 1077387582 bp ( 37.29 % ) Sampling Time: 00:16:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 18:55:58 (hh:mm:ss) Elapsed Time, 163721 HSPs Collected Number of families returned by RECON: 74551 Round Time: 19:49:06 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatScout/RECON discovery complete: 332 families found Classification Time: 00:15:16 (hh:mm:ss) Elapsed Time Program Time: 23:48:35 (hh:mm:ss) Elapsed Time