RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.ZE4MZu/RM_1231413.SatSep130509452025 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: 1757765384 Database = /dev/shm/rModeler.ZE4MZu/GCA_902702905.1_Austropuccinia_psidii - Sequences = 66 - Bases = 1018398822 Storage Throughput = excellent ( 1142.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047882 bp ( 40036382 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 167 raw families identified - RepeatScout: Running filtering stage.. 142 families remaining - RepeatScout: 00:14:37 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 142 families... 00:37:04 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 8 satellite(s), 44 contained, found in 00:00:06 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:07 (hh:mm:ss) Elapsed Time Round Time: 00:52:57 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5422 repeats masked totaling 7500062 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041166 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10038366 bp After Masking: 2444911 bp Masked: 75.64 % -- Input Database Coverage: 10041166 bp out of 1018398822 bp ( 0.99 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 70706 HSPs Collected Number of families returned by RECON: 331 Round Time: 00:18:38 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15296 repeats masked totaling 23600563 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046641 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30037941 bp After Masking: 6142387 bp Masked: 79.55 % -- Input Database Coverage: 40087807 bp out of 1018398822 bp ( 3.94 % ) Sampling Time: 00:05:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:19:21 (hh:mm:ss) Elapsed Time, 17811 HSPs Collected Number of families returned by RECON: 1055 Round Time: 00:26:44 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46479 repeats masked totaling 72855804 bp(s). - TE Masking time 00:08:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90066443 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90038380 bp After Masking: 16435184 bp Masked: 81.75 % -- Input Database Coverage: 130154250 bp out of 1018398822 bp ( 12.78 % ) Sampling Time: 00:17:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:29:53 (hh:mm:ss) Elapsed Time, 111645 HSPs Collected Number of families returned by RECON: 2858 Round Time: 01:53:54 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153732 repeats masked totaling 228994591 bp(s). - TE Masking time 00:53:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270090621 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 270009380 bp After Masking: 38725211 bp Masked: 85.66 % -- Input Database Coverage: 400244871 bp out of 1018398822 bp ( 39.30 % ) Sampling Time: 01:19:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 08:06:10 (hh:mm:ss) Elapsed Time, 360165 HSPs Collected Number of families returned by RECON: 7014 Round Time: 09:42:06 (hh:mm:ss) Elapsed Time : 311 families discovered. RepeatScout/RECON discovery complete: 548 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.ZE4MZu/RM_1231413.SatSep130509452025 # 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: 00:09:49 (hh:mm:ss) Elapsed Time Program Time: 13:24:08 (hh:mm:ss) Elapsed Time