RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rdSXlX/RM_17296.MonJan20503022023 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: 1672664581 Database = /dev/shm/rModeler.rdSXlX/GCA_905171665.2_fTraTra1.2 - Sequences = 153 - Bases = 801243942 - N50 = 35709794 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38037947-40754244 |* [ 4 ] 35321651-38037947 |** [ 7 ] 32605354-35321650 |* [ 4 ] 29889058-32605354 | [ 2 ] 27172762-29889058 |* [ 3 ] 24456465-27172761 |* [ 3 ] 21740169-24456465 | [ ] 19023872-21740168 | [ ] 16307576-19023872 | [ ] 13591280-16307576 | [ 1 ] 10874983-13591279 | [ ] 8158687-10874983 | [ ] 5442390-8158686 | [ ] 2726094-5442390 | [ ] 9798-2726094 |************************************************** [ 129 ] Storage Throughput = excellent ( 1140.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032943 bp ( 40031059 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:46 (hh:mm:ss) Elapsed Time Round Time: 00:27:33 (hh:mm:ss) Elapsed Time : 670 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8630 repeats masked totaling 1768861 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008712 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10008643 bp After Masking: 7916341 bp Masked: 20.90 % -- Input Database Coverage: 10008712 bp out of 801243942 bp ( 1.25 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:26 (hh:mm:ss) Elapsed Time, 7919 HSPs Collected Number of families returned by RECON: 1655 Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24786 repeats masked totaling 4932003 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024151 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30022336 bp After Masking: 24080982 bp Masked: 19.79 % -- Input Database Coverage: 40032863 bp out of 801243942 bp ( 5.00 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:36:15 (hh:mm:ss) Elapsed Time, 44659 HSPs Collected Number of families returned by RECON: 6056 Round Time: 00:42:02 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80867 repeats masked totaling 16039022 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017985 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90015101 bp After Masking: 70787589 bp Masked: 21.36 % -- Input Database Coverage: 130050848 bp out of 801243942 bp ( 16.23 % ) Sampling Time: 00:11:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:20:49 (hh:mm:ss) Elapsed Time, 375108 HSPs Collected Number of families returned by RECON: 22524 Round Time: 04:54:36 (hh:mm:ss) Elapsed Time : 629 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 315692 repeats masked totaling 63317511 bp(s). - TE Masking time 00:15:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035446 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270025379 bp After Masking: 197309545 bp Masked: 26.93 % -- Input Database Coverage: 400086294 bp out of 801243942 bp ( 49.93 % ) Sampling Time: 00:39:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 32:53:40 (hh:mm:ss) Elapsed Time, 1226667 HSPs Collected Number of families returned by RECON: 80799 Round Time: 36:55:23 (hh:mm:ss) Elapsed Time : 1713 families discovered. RepeatScout/RECON discovery complete: 3083 families found Classification Time: 02:32:20 (hh:mm:ss) Elapsed Time Program Time: 45:40:15 (hh:mm:ss) Elapsed Time