RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.GxdzsD/RM_502549.ThuMar191017062026 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: 1773940626 Database = /dev/shm/rModeler.GxdzsD/GCA_024363595.1_UCB_Xborealis_1 - Sequences = 23435 - Bases = 2747450723 - N50 = 153391691 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215390541-230775509 | [ 1 ] 200005574-215390541 | [ ] 184620607-200005574 | [ 1 ] 169235639-184620606 | [ 2 ] 153850672-169235639 | [ 2 ] 138465705-153850672 | [ 2 ] 123080738-138465705 | [ 6 ] 107695770-123080737 | [ 2 ] 92310803-107695770 | [ 2 ] 76925836-92310803 | [ ] 61540869-76925836 | [ ] 46155901-61540868 | [ ] 30770934-46155901 | [ ] 15385967-30770934 | [ ] 1000-15385967 |************************************************** [ 23417 ] Storage Throughput = excellent ( 1080.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 49766298 bp ( 40034117 non ambiguous ) - Num Contigs Represented = 499 - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 429 raw families identified - RepeatScout: Running filtering stage.. 412 families remaining - RepeatScout: 00:04:37 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 400 families... 00:01:34 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 180 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:11:22 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14253 repeats masked totaling 2671133 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12302504 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 10008563 bp After Masking: 7210802 bp Masked: 27.95 % -- Input Database Coverage: 12302504 bp out of 2747450723 bp ( 0.45 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 89676 Comparison Time: 00:08:33 (hh:mm:ss) Elapsed Time, 333883 HSPs Collected Number of families returned by RECON: 2427 Round Time: 00:18:07 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60669 repeats masked totaling 11190695 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 37463792 bp Num Contigs Represented = 364 Non ambiguous bp: Initial: 30025552 bp After Masking: 18519910 bp Masked: 38.32 % -- Input Database Coverage: 49766296 bp out of 2747450723 bp ( 1.81 % ) Sampling Time: 00:05:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 769420 Comparison Time: 00:36:14 (hh:mm:ss) Elapsed Time, 76532 HSPs Collected Number of families returned by RECON: 3978 Round Time: 00:44:48 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 201258 repeats masked totaling 36523951 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 113476269 bp Num Contigs Represented = 995 Non ambiguous bp: Initial: 90008032 bp After Masking: 52574582 bp Masked: 41.59 % -- Input Database Coverage: 163242565 bp out of 2747450723 bp ( 5.94 % ) Sampling Time: 00:16:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 6924781 Comparison Time: 04:02:49 (hh:mm:ss) Elapsed Time, 176561 HSPs Collected Number of families returned by RECON: 12299 Round Time: 04:27:55 (hh:mm:ss) Elapsed Time : 381 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:33:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 688567 repeats masked totaling 121544527 bp(s). - TE Masking time 00:12:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 336703880 bp Num Contigs Represented = 2982 Non ambiguous bp: Initial: 270019417 bp After Masking: 145865093 bp Masked: 45.98 % -- Input Database Coverage: 499946445 bp out of 2747450723 bp ( 18.20 % ) Sampling Time: 00:54:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 61488505 Comparison Time: 29:48:36 (hh:mm:ss) Elapsed Time, 431261 HSPs Collected Number of families returned by RECON: 42867 Round Time: 31:41:08 (hh:mm:ss) Elapsed Time : 870 families discovered. RepeatScout/RECON discovery complete: 1643 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.GxdzsD/RM_502549.ThuMar191017062026 # 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: 00:05:47 (hh:mm:ss) Elapsed Time Program Time: 37:29:07 (hh:mm:ss) Elapsed Time