RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SCZqjh/RM_1196349.SunJul70818422024 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: 1720365521 Database = /dev/shm/rModeler.SCZqjh/GCF_033807715.1_fColSai1.1 - Sequences = 759 - Bases = 1146362327 - N50 = 48275806 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 53786346-57628157 | [ 3 ] 49944536-53786346 | [ 3 ] 46102725-49944535 | [ 9 ] 42260915-46102725 | [ 3 ] 38419104-42260914 | [ 3 ] 34577294-38419104 | [ 2 ] 30735483-34577293 | [ ] 26893673-30735483 | [ 1 ] 23051862-26893672 | [ ] 19210052-23051862 | [ ] 15368241-19210051 | [ ] 11526431-15368241 | [ ] 7684620-11526430 | [ ] 3842810-7684620 | [ ] 1000-3842810 |************************************************** [ 735 ] Storage Throughput = excellent ( 1171.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040361 bp ( 40025468 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:43 (hh:mm:ss) Elapsed Time Round Time: 00:26:14 (hh:mm:ss) Elapsed Time : 988 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 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14368 repeats masked totaling 3109826 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006841 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10004341 bp After Masking: 6147062 bp Masked: 38.56 % -- Input Database Coverage: 10006841 bp out of 1146362327 bp ( 0.87 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 14971 HSPs Collected Number of families returned by RECON: 1383 Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47416 repeats masked totaling 10191512 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033440 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30021047 bp After Masking: 17131721 bp Masked: 42.93 % -- Input Database Coverage: 40040281 bp out of 1146362327 bp ( 3.49 % ) Sampling Time: 00:07:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:24:15 (hh:mm:ss) Elapsed Time, 46925 HSPs Collected Number of families returned by RECON: 4554 Round Time: 00:32:47 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151313 repeats masked totaling 31680299 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90064708 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90031708 bp After Masking: 50785993 bp Masked: 43.59 % -- Input Database Coverage: 130104989 bp out of 1146362327 bp ( 11.35 % ) Sampling Time: 00:19:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 02:23:03 (hh:mm:ss) Elapsed Time, 298673 HSPs Collected Number of families returned by RECON: 12631 Round Time: 02:51:06 (hh:mm:ss) Elapsed Time : 612 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 516880 repeats masked totaling 108695532 bp(s). - TE Masking time 00:13:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270120867 bp Num Contigs Represented = 256 Non ambiguous bp: Initial: 270006303 bp After Masking: 138439153 bp Masked: 48.73 % -- Input Database Coverage: 400225856 bp out of 1146362327 bp ( 34.91 % ) Sampling Time: 01:05:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23629375 Comparison Time: 15:57:49 (hh:mm:ss) Elapsed Time, 776479 HSPs Collected Number of families returned by RECON: 37183 Round Time: 17:53:18 (hh:mm:ss) Elapsed Time : 1431 families discovered. RepeatScout/RECON discovery complete: 3170 families found Classification Time: 02:11:42 (hh:mm:ss) Elapsed Time Program Time: 24:03:06 (hh:mm:ss) Elapsed Time