RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.8ctFoI/RM_1968647.ThuSep112150442025 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: 1757652644 Database = /data/tmp/rModeler.8ctFoI/GCA_027627245.1_Physisporinus_sp_VT162_reassembly_enz - Sequences = 2700 - Bases = 46923322 - N50 = 51186 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 280120-300106 | [ 1 ] 260135-280120 | [ 1 ] 240149-260134 | [ 2 ] 220164-240149 | [ ] 200178-220163 | [ 1 ] 180193-200178 | [ 2 ] 160207-180192 | [ 5 ] 140222-160207 | [ 15 ] 120236-140221 | [ 20 ] 100251-120236 | [ 22 ] 80265-100250 |* [ 51 ] 60280-80265 |** [ 89 ] 40294-60279 |**** [ 174 ] 20309-40294 |******* [ 312 ] 324-20309 |************************************************** [ 2005 ] Storage Throughput = good ( 905.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041756 bp ( 40025020 non ambiguous ) - Num Contigs Represented = 2382 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 246 raw families identified - RepeatScout: Running filtering stage.. 235 families remaining - RepeatScout: 00:01:25 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 231 families... 00:00:58 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 52 contained, found in 00:00:13 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:13 (hh:mm:ss) Elapsed Time Round Time: 00:02:46 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1654 repeats masked totaling 708696 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005115 bp Num Contigs Represented = 676 Non ambiguous bp: Initial: 10000935 bp After Masking: 9255013 bp Masked: 7.46 % -- Input Database Coverage: 10005115 bp out of 46923322 bp ( 21.32 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 253828 Comparison Time: 00:07:56 (hh:mm:ss) Elapsed Time, 3503 HSPs Collected Number of families returned by RECON: 837 Round Time: 00:09:02 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5007 repeats masked totaling 2160962 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036597 bp Num Contigs Represented = 1835 Non ambiguous bp: Initial: 30024041 bp After Masking: 27766374 bp Masked: 7.52 % -- Input Database Coverage: 40041712 bp out of 46923322 bp ( 85.33 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2218671 Comparison Time: 00:35:20 (hh:mm:ss) Elapsed Time, 30498 HSPs Collected Number of families returned by RECON: 3763 Round Time: 00:40:40 (hh:mm:ss) Elapsed Time : 17 families discovered. - Increasing sample size to include end piece now = 96918207 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 96918207 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1125 repeats masked totaling 485911 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 6881421 bp Num Contigs Represented = 440 Non ambiguous bp: Initial: 6877723 bp After Masking: 6368498 bp Masked: 7.40 % -- Input Database Coverage: 46923133 bp out of 46923322 bp ( 100.00 % ) Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 105570 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 1544 HSPs Collected Number of families returned by RECON: 430 Round Time: 00:05:30 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 198 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.8ctFoI/RM_1968647.ThuSep112150442025 # 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: 00:01:14 (hh:mm:ss) Elapsed Time Program Time: 00:59:12 (hh:mm:ss) Elapsed Time