RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.mGUHQh/RM_214896.TueSep90555592025 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: 1757422559 Database = /dev/shm/rModeler.mGUHQh/GCA_009663115.1_ASM966311v1 - Sequences = 12 - Bases = 45614948 Storage Throughput = excellent ( 1678.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40089264 bp ( 40003909 non ambiguous ) - Num Contigs Represented = 12 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 37 raw families identified - RepeatScout: Running filtering stage.. 33 families remaining - RepeatScout: 00:00:56 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 31 families... 00:55:00 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time Round Time: 00:56:05 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (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... 734 repeats masked totaling 716118 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10047246 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10015981 bp After Masking: 9286478 bp Masked: 7.28 % -- Input Database Coverage: 10047246 bp out of 45614948 bp ( 22.03 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 3187 HSPs Collected Number of families returned by RECON: 577 Round Time: 00:16:18 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2225 repeats masked totaling 1838566 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30081938 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 30027847 bp After Masking: 28155381 bp Masked: 6.24 % -- Input Database Coverage: 40129184 bp out of 45614948 bp ( 87.97 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:14:32 (hh:mm:ss) Elapsed Time, 8870 HSPs Collected Number of families returned by RECON: 2856 Round Time: 00:17:51 (hh:mm:ss) Elapsed Time : 5 families discovered. - Increasing sample size to include end piece now = 95567702 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 95567702 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 478 repeats masked totaling 410765 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 5485522 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 5476133 bp After Masking: 5059647 bp Masked: 7.61 % -- Input Database Coverage: 45614706 bp out of 45614948 bp ( 100.00 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 9453 Comparison Time: 00:01:41 (hh:mm:ss) Elapsed Time, 310 HSPs Collected Number of families returned by RECON: 198 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 40 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.mGUHQh/RM_214896.TueSep90555592025 # 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: 00:00:20 (hh:mm:ss) Elapsed Time Program Time: 01:34:12 (hh:mm:ss) Elapsed Time