RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.eN8dWZ/RM_17131.SatDec70422432024 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: 1733574161 Database = /scratch/tmp/rModeler.eN8dWZ/GCA_037950955.1_bSarPap1.hap2 - Sequences = 140 - Bases = 1469241744 - N50 = 99015716 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 221117196-236910404 | [ 1 ] 205323989-221117196 | [ ] 189530782-205323989 | [ 1 ] 173737574-189530781 | [ ] 157944367-173737574 | [ ] 142151160-157944367 | [ 1 ] 126357953-142151160 | [ ] 110564745-126357952 | [ ] 94771538-110564745 | [ 1 ] 78978331-94771538 | [ 1 ] 63185124-78978331 | [ ] 47391916-63185123 | [ 2 ] 31598709-47391916 | [ 2 ] 15805502-31598709 |*** [ 8 ] 12295-15805502 |************************************************** [ 123 ] Storage Throughput = fair ( 643.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027289 bp ( 40026889 non ambiguous ) - Num Contigs Represented = 74 - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:31:01 (hh:mm:ss) Elapsed Time Round Time: 00:37:42 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 980 repeats masked totaling 352887 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002856 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10002656 bp After Masking: 7436696 bp Masked: 25.65 % -- Input Database Coverage: 10002856 bp out of 1469241744 bp ( 0.68 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:33 (hh:mm:ss) Elapsed Time, 1941 HSPs Collected Number of families returned by RECON: 206 Round Time: 00:07:30 (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 : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3615 repeats masked totaling 1278104 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024427 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30024227 bp After Masking: 22844589 bp Masked: 23.91 % -- Input Database Coverage: 40027283 bp out of 1469241744 bp ( 2.72 % ) Sampling Time: 00:05:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:42 (hh:mm:ss) Elapsed Time, 21279 HSPs Collected Number of families returned by RECON: 1240 Round Time: 00:38:22 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11675 repeats masked totaling 4762363 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017781 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90015581 bp After Masking: 65292934 bp Masked: 27.46 % -- Input Database Coverage: 130045064 bp out of 1469241744 bp ( 8.85 % ) Sampling Time: 00:17:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:25:51 (hh:mm:ss) Elapsed Time, 56621 HSPs Collected Number of families returned by RECON: 5915 Round Time: 04:18:59 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48841 repeats masked totaling 17728307 bp(s). - TE Masking time 00:03:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031322 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270027322 bp After Masking: 196773124 bp Masked: 27.13 % -- Input Database Coverage: 400076386 bp out of 1469241744 bp ( 27.23 % ) Sampling Time: 00:51:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 27:48:00 (hh:mm:ss) Elapsed Time, 372995 HSPs Collected Number of families returned by RECON: 38264 Round Time: 29:27:16 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatScout/RECON discovery complete: 311 families found Classification Time: 00:36:32 (hh:mm:ss) Elapsed Time Program Time: 35:46:21 (hh:mm:ss) Elapsed Time