RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.5oVziN/RM_530944.TueSep22005142025 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: 1756868713 Database = /dev/shm/rModeler.5oVziN/GCA_032719375.1_Trm_1.0 - Sequences = 79 - Bases = 1295808506 Storage Throughput = excellent ( 1093.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006115 bp ( 40006115 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 140 raw families identified - RepeatScout: Running filtering stage.. 121 families remaining - RepeatScout: 00:05:51 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 113 families... 02:42:47 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 3 satellite(s), 31 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 02:49:29 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2469 repeats masked totaling 864054 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002634 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10002634 bp After Masking: 8944197 bp Masked: 10.58 % -- Input Database Coverage: 10002634 bp out of 1295808506 bp ( 0.77 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:38 (hh:mm:ss) Elapsed Time, 832 HSPs Collected Number of families returned by RECON: 213 Round Time: 00:07:51 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7263 repeats masked totaling 2544700 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003401 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30003401 bp After Masking: 26603968 bp Masked: 11.33 % -- Input Database Coverage: 40006035 bp out of 1295808506 bp ( 3.09 % ) Sampling Time: 00:07:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:38:52 (hh:mm:ss) Elapsed Time, 5438 HSPs Collected Number of families returned by RECON: 1246 Round Time: 00:46:50 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22772 repeats masked totaling 7606323 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003315 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90003015 bp After Masking: 79919345 bp Masked: 11.20 % -- Input Database Coverage: 130009350 bp out of 1295808506 bp ( 10.03 % ) Sampling Time: 00:14:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:54:01 (hh:mm:ss) Elapsed Time, 40101 HSPs Collected Number of families returned by RECON: 7831 Round Time: 05:11:45 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 88902 repeats masked totaling 27178364 bp(s). - TE Masking time 00:07:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031563 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 270031163 bp After Masking: 235646808 bp Masked: 12.73 % -- Input Database Coverage: 400040913 bp out of 1295808506 bp ( 30.87 % ) Sampling Time: 00:45:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 39:57:41 (hh:mm:ss) Elapsed Time, 302257 HSPs Collected Number of families returned by RECON: 48237 Round Time: 41:26:00 (hh:mm:ss) Elapsed Time : 238 families discovered. RepeatScout/RECON discovery complete: 383 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.5oVziN/RM_530944.TueSep22005142025 # 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: 00:07:44 (hh:mm:ss) Elapsed Time Program Time: 50:29:39 (hh:mm:ss) Elapsed Time