RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.bhBHMT/RM_3505042.ThuSep111018562025 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: 1757611136 Database = /dev/shm/rModeler.bhBHMT/GCA_024321985.1_QSMG - Sequences = 37 - Bases = 48323753 Storage Throughput = excellent ( 1679.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019089 bp ( 40019089 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 294 raw families identified - RepeatScout: Running filtering stage.. 279 families remaining - RepeatScout: 00:01:20 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 272 families... 00:02:48 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 11 satellite(s), 85 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time Round Time: 00:04:16 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (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... 2711 repeats masked totaling 1635920 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038132 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10038132 bp After Masking: 8270761 bp Masked: 17.61 % -- Input Database Coverage: 10038132 bp out of 48323753 bp ( 20.77 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 6083 HSPs Collected Number of families returned by RECON: 983 Round Time: 00:03:47 (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 : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7888 repeats masked totaling 5036424 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020919 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30020919 bp After Masking: 24620596 bp Masked: 17.99 % -- Input Database Coverage: 40059051 bp out of 48323753 bp ( 82.90 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:13:44 (hh:mm:ss) Elapsed Time, 29907 HSPs Collected Number of families returned by RECON: 3922 Round Time: 00:15:04 (hh:mm:ss) Elapsed Time : 19 families discovered. - Increasing sample size to include end piece now = 98285621 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 98285621 bp - Sequence extraction : 00:00:00 (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... 2259 repeats masked totaling 1290261 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 8264507 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 8264507 bp After Masking: 6821884 bp Masked: 17.46 % -- Input Database Coverage: 48323558 bp out of 48323753 bp ( 100.00 % ) Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 21115 Comparison Time: 00:02:38 (hh:mm:ss) Elapsed Time, 2002 HSPs Collected Number of families returned by RECON: 722 Round Time: 00:02:58 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 200 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.bhBHMT/RM_3505042.ThuSep111018562025 # 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: 00:01:06 (hh:mm:ss) Elapsed Time Program Time: 00:27:11 (hh:mm:ss) Elapsed Time