RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.38xzve/RM_2387306.ThuSep110929002025 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: 1757608139 Database = /dev/shm/rModeler.38xzve/GCA_023105775.2_Au3_v3_hapB - Sequences = 17 - Bases = 982558553 Storage Throughput = excellent ( 1140.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040579 bp ( 40038579 non ambiguous ) - Num Contigs Represented = 17 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 182 raw families identified - RepeatScout: Running filtering stage.. 164 families remaining - RepeatScout: 00:15:15 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 163 families... 00:48:09 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 58 contained, found in 00:00:08 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 01:04:47 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6081 repeats masked totaling 7113945 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040280 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10039280 bp After Masking: 2820759 bp Masked: 71.90 % -- Input Database Coverage: 10040280 bp out of 982558553 bp ( 1.02 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 172903 HSPs Collected Number of families returned by RECON: 340 Round Time: 00:59:33 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15670 repeats masked totaling 24503836 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040299 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 30039299 bp After Masking: 5251320 bp Masked: 82.52 % -- Input Database Coverage: 40080579 bp out of 982558553 bp ( 4.08 % ) Sampling Time: 00:06:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:16:05 (hh:mm:ss) Elapsed Time, 24542 HSPs Collected Number of families returned by RECON: 976 Round Time: 00:23:40 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51107 repeats masked totaling 74008209 bp(s). - TE Masking time 00:10:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038673 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 90037173 bp After Masking: 15102265 bp Masked: 83.23 % -- Input Database Coverage: 130119252 bp out of 982558553 bp ( 13.24 % ) Sampling Time: 00:20:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:29:26 (hh:mm:ss) Elapsed Time, 98682 HSPs Collected Number of families returned by RECON: 2827 Round Time: 01:56:33 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 167530 repeats masked totaling 231617386 bp(s). - TE Masking time 01:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044398 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 270039398 bp After Masking: 35308903 bp Masked: 86.92 % -- Input Database Coverage: 400163650 bp out of 982558553 bp ( 40.73 % ) Sampling Time: 01:35:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 07:58:29 (hh:mm:ss) Elapsed Time, 242131 HSPs Collected Number of families returned by RECON: 6449 Round Time: 09:51:26 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatScout/RECON discovery complete: 521 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.38xzve/RM_2387306.ThuSep110929002025 # 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: 00:10:11 (hh:mm:ss) Elapsed Time Program Time: 14:26:10 (hh:mm:ss) Elapsed Time