RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.geZR1V/RM_3566377.WedMar270835312024 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: 1711553731 Database = /dev/shm/rModeler.geZR1V/GCA_963854745.1_fScoMax1.1 - Sequences = 108 - Bases = 550297089 - N50 = 26177324 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30853504-33057255 |* [ 3 ] 28649754-30853504 | [ 1 ] 26446004-28649754 |* [ 2 ] 24242253-26446003 |**** [ 7 ] 22038503-24242253 |** [ 4 ] 19834753-22038503 |* [ 3 ] 17631002-19834752 | [ ] 15427252-17631002 |* [ 2 ] 13223502-15427252 | [ ] 11019751-13223501 | [ ] 8816001-11019751 | [ ] 6612251-8816001 | [ ] 4408500-6612250 | [ ] 2204750-4408500 | [ ] 1000-2204750 |************************************************** [ 86 ] Storage Throughput = excellent ( 1381.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042748 bp ( 40030988 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:37 (hh:mm:ss) Elapsed Time Round Time: 00:20:01 (hh:mm:ss) Elapsed Time : 303 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4590 repeats masked totaling 563094 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042511 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10039511 bp After Masking: 8959636 bp Masked: 10.76 % -- Input Database Coverage: 10042511 bp out of 550297089 bp ( 1.82 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:41 (hh:mm:ss) Elapsed Time, 5743 HSPs Collected Number of families returned by RECON: 1316 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14537 repeats masked totaling 1898287 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040217 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30031457 bp After Masking: 26401419 bp Masked: 12.09 % -- Input Database Coverage: 40082728 bp out of 550297089 bp ( 7.28 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:32:32 (hh:mm:ss) Elapsed Time, 45798 HSPs Collected Number of families returned by RECON: 5303 Round Time: 00:37:16 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53879 repeats masked totaling 7449049 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90052145 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90025584 bp After Masking: 77636894 bp Masked: 13.76 % -- Input Database Coverage: 130134873 bp out of 550297089 bp ( 23.65 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:31:48 (hh:mm:ss) Elapsed Time, 208813 HSPs Collected Number of families returned by RECON: 19739 Round Time: 03:52:48 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 208027 repeats masked totaling 30004303 bp(s). - TE Masking time 00:04:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270096449 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270019802 bp After Masking: 223406952 bp Masked: 17.26 % -- Input Database Coverage: 400231322 bp out of 550297089 bp ( 72.73 % ) Sampling Time: 00:38:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 26:28:09 (hh:mm:ss) Elapsed Time, 753257 HSPs Collected Number of families returned by RECON: 78032 Round Time: 28:50:26 (hh:mm:ss) Elapsed Time : 903 families discovered. RepeatScout/RECON discovery complete: 1648 families found Classification Time: 00:58:03 (hh:mm:ss) Elapsed Time Program Time: 34:46:38 (hh:mm:ss) Elapsed Time