RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.bivI9H/RM_660629.ThuDec50522122024 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: 1733404932 Database = /scratch/tmp/rModeler.bivI9H/GCA_964211795.1_bAytFer1.hap2.1 - Sequences = 362 - Bases = 1103588439 - N50 = 121053116 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193561793-207387564 | [ 1 ] 179736022-193561792 | [ ] 165910251-179736021 | [ ] 152084480-165910250 | [ 1 ] 138258709-152084479 | [ ] 124432938-138258708 | [ ] 110607167-124432937 | [ 1 ] 96781396-110607166 | [ ] 82955625-96781395 | [ ] 69129854-82955624 | [ 1 ] 55304083-69129853 | [ 1 ] 41478312-55304082 | [ ] 27652541-41478311 | [ 4 ] 13826770-27652540 |* [ 9 ] 1000-13826770 |************************************************** [ 344 ] Storage Throughput = excellent ( 1528.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024363 bp ( 40022163 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:42 (hh:mm:ss) Elapsed Time Round Time: 00:13:04 (hh:mm:ss) Elapsed Time : 67 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 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1590 repeats masked totaling 690613 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007080 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10007080 bp After Masking: 8811915 bp Masked: 11.94 % -- Input Database Coverage: 10007080 bp out of 1103588439 bp ( 0.91 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:34 (hh:mm:ss) Elapsed Time, 925 HSPs Collected Number of families returned by RECON: 277 Round Time: 00:05:43 (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 : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5759 repeats masked totaling 2401387 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017203 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30015003 bp After Masking: 26261363 bp Masked: 12.51 % -- Input Database Coverage: 40024283 bp out of 1103588439 bp ( 3.63 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:18:58 (hh:mm:ss) Elapsed Time, 21153 HSPs Collected Number of families returned by RECON: 1713 Round Time: 00:24:36 (hh:mm:ss) Elapsed Time : 7 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 00:12:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17727 repeats masked totaling 6714611 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028637 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 90021237 bp After Masking: 79239658 bp Masked: 11.98 % -- Input Database Coverage: 130052920 bp out of 1103588439 bp ( 11.78 % ) Sampling Time: 00:14:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:07:05 (hh:mm:ss) Elapsed Time, 62361 HSPs Collected Number of families returned by RECON: 10509 Round Time: 02:24:49 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61003 repeats masked totaling 23560962 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270054140 bp Num Contigs Represented = 194 Non ambiguous bp: Initial: 270033438 bp After Masking: 233932203 bp Masked: 13.37 % -- Input Database Coverage: 400107060 bp out of 1103588439 bp ( 36.26 % ) Sampling Time: 00:47:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 16:23:21 (hh:mm:ss) Elapsed Time, 392717 HSPs Collected Number of families returned by RECON: 65045 Round Time: 18:08:56 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatScout/RECON discovery complete: 349 families found Classification Time: 00:14:46 (hh:mm:ss) Elapsed Time Program Time: 21:31:54 (hh:mm:ss) Elapsed Time