RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.1fnuGy/RM_642388.MonFeb91419412026 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1770675581 Database = /dev/shm/rModeler.1fnuGy/GCA_964261705.1_iuLoeVari1.hap1.1 - Sequences = 404 - Bases = 531439522 - N50 = 66175113 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 67348731-72159284 | [ 2 ] 62538179-67348731 | [ 2 ] 57727627-62538179 | [ 1 ] 52917074-57727626 | [ 1 ] 48106522-52917074 | [ ] 43295970-48106522 | [ 2 ] 38485418-43295970 | [ ] 33674865-38485417 | [ 1 ] 28864313-33674865 | [ ] 24053761-28864313 | [ ] 19243209-24053761 | [ ] 14432656-19243208 | [ ] 9622104-14432656 | [ ] 4811552-9622104 | [ ] 1000-4811552 |************************************************** [ 395 ] Storage Throughput = excellent ( 1439.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40056156 bp ( 40025696 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 750 raw families identified - RepeatScout: Running filtering stage.. 720 families remaining - RepeatScout: 00:04:35 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 701 families... 01:38:40 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 23 satellite(s), 238 contained, found in 00:00:09 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 01:43:52 (hh:mm:ss) Elapsed Time : 441 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20562 repeats masked totaling 4582069 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040413 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10033613 bp After Masking: 5198053 bp Masked: 48.19 % -- Input Database Coverage: 10040413 bp out of 531439522 bp ( 1.89 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:25 (hh:mm:ss) Elapsed Time, 115217 HSPs Collected Number of families returned by RECON: 1417 Round Time: 00:04:43 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66177 repeats masked totaling 14581016 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30055667 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30032007 bp After Masking: 14708094 bp Masked: 51.03 % -- Input Database Coverage: 40096080 bp out of 531439522 bp ( 7.54 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:15:53 (hh:mm:ss) Elapsed Time, 1342482 HSPs Collected Number of families returned by RECON: 3695 Round Time: 00:18:03 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 218434 repeats masked totaling 46118916 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90108934 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90039786 bp After Masking: 41615860 bp Masked: 53.78 % -- Input Database Coverage: 130205014 bp out of 531439522 bp ( 24.50 % ) Sampling Time: 00:04:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 01:22:58 (hh:mm:ss) Elapsed Time, 8632722 HSPs Collected Number of families returned by RECON: 9196 Round Time: 01:32:41 (hh:mm:ss) Elapsed Time : 514 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 749843 repeats masked totaling 155143195 bp(s). - TE Masking time 00:11:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270230820 bp Num Contigs Represented = 249 Non ambiguous bp: Initial: 270036880 bp After Masking: 108153827 bp Masked: 59.95 % -- Input Database Coverage: 400435834 bp out of 531439522 bp ( 75.35 % ) Sampling Time: 00:18:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23546953 Comparison Time: 09:55:18 (hh:mm:ss) Elapsed Time, 105805576 HSPs Collected Number of families returned by RECON: 21000 Round Time: 10:56:31 (hh:mm:ss) Elapsed Time : 991 families discovered. RepeatScout/RECON discovery complete: 2113 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.1fnuGy/RM_642388.MonFeb91419412026 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:06:39 (hh:mm:ss) Elapsed Time Program Time: 14:42:29 (hh:mm:ss) Elapsed Time