RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.wGb9ri/RM_1737668.TueJun231515472026 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: 1782252937 Database = /data/tmp/rModeler.wGb9ri/GCF_964638095.1_fPorCra3.hap1.1 - Sequences = 2788 - Bases = 1630001977 - N50 = 55491621 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 122780267-131550215 | [ 2 ] 114010319-122780266 | [ ] 105240372-114010319 | [ ] 96470424-105240371 | [ 1 ] 87700476-96470423 | [ ] 78930529-87700476 | [ ] 70160581-78930528 | [ 1 ] 61390633-70160580 | [ 2 ] 52620686-61390633 | [ 5 ] 43850738-52620685 | [ 4 ] 35080790-43850737 | [ 2 ] 26310843-35080790 | [ 4 ] 17540895-26310842 | [ 8 ] 8770947-17540894 | [ 1 ] 1000-8770947 |************************************************** [ 2758 ] Storage Throughput = excellent ( 1901.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047518 bp ( 40035318 non ambiguous ) - Num Contigs Represented = 185 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 1353 raw families identified - RepeatScout: Running filtering stage.. 1235 families remaining - RepeatScout: 00:06:38 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 1192 families... 00:23:51 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 16 satellite(s), 497 contained, found in 00:00:22 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:22 (hh:mm:ss) Elapsed Time Round Time: 00:31:30 (hh:mm:ss) Elapsed Time : 680 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 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15652 repeats masked totaling 3158708 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032652 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 10028052 bp After Masking: 5260364 bp Masked: 47.54 % -- Input Database Coverage: 10032652 bp out of 1630001977 bp ( 0.62 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:13:47 (hh:mm:ss) Elapsed Time, 23294 HSPs Collected Number of families returned by RECON: 1848 Round Time: 00:17:42 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49373 repeats masked totaling 10181674 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014786 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 30007186 bp After Masking: 14836431 bp Masked: 50.56 % -- Input Database Coverage: 40047438 bp out of 1630001977 bp ( 2.46 % ) Sampling Time: 00:05:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 310078 Comparison Time: 00:26:53 (hh:mm:ss) Elapsed Time, 85521 HSPs Collected Number of families returned by RECON: 5889 Round Time: 00:35:33 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 169762 repeats masked totaling 33162865 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059096 bp Num Contigs Represented = 328 Non ambiguous bp: Initial: 90023609 bp After Masking: 41678168 bp Masked: 53.70 % -- Input Database Coverage: 130106534 bp out of 1630001977 bp ( 7.98 % ) Sampling Time: 00:18:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2717946 Comparison Time: 01:54:06 (hh:mm:ss) Elapsed Time, 402856 HSPs Collected Number of families returned by RECON: 15180 Round Time: 02:20:57 (hh:mm:ss) Elapsed Time : 744 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 620729 repeats masked totaling 120526798 bp(s). - TE Masking time 00:13:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270125747 bp Num Contigs Represented = 771 Non ambiguous bp: Initial: 270027839 bp After Masking: 104607909 bp Masked: 61.26 % -- Input Database Coverage: 400232281 bp out of 1630001977 bp ( 24.55 % ) Sampling Time: 00:49:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24489501 Comparison Time: 12:53:32 (hh:mm:ss) Elapsed Time, 991032 HSPs Collected Number of families returned by RECON: 36578 Round Time: 14:18:58 (hh:mm:ss) Elapsed Time : 1650 families discovered. RepeatScout/RECON discovery complete: 3283 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.wGb9ri/RM_1737668.TueJun231515472026 # 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: 00:08:58 (hh:mm:ss) Elapsed Time Program Time: 18:13:38 (hh:mm:ss) Elapsed Time