RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.GltrIi/RM_3729401.WedSep100128472025 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: 1757492926 Database = /data/tmp/rModeler.GltrIi/GCA_013363175.1_ASM1336317v1 - Sequences = 3852 - Bases = 45367990 - N50 = 30752 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 260754-279344 | [ 1 ] 242164-260754 | [ ] 223574-242164 | [ ] 204984-223574 | [ ] 186394-204984 | [ ] 167804-186394 | [ 3 ] 149214-167804 | [ 3 ] 130624-149214 | [ 5 ] 112034-130624 | [ 9 ] 93444-112034 | [ 16 ] 74854-93444 | [ 32 ] 56264-74854 | [ 60 ] 37674-56264 |** [ 161 ] 19084-37674 |******* [ 450 ] 494-19084 |************************************************** [ 3112 ] Storage Throughput = good ( 997.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010076 bp ( 40003868 non ambiguous ) - Num Contigs Represented = 3470 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 128 raw families identified - RepeatScout: Running filtering stage.. 113 families remaining - RepeatScout: 00:01:36 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 107 families... 00:00:24 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 22 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:02:10 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 909 repeats masked totaling 218620 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027411 bp Num Contigs Represented = 912 Non ambiguous bp: Initial: 10025997 bp After Masking: 9789252 bp Masked: 2.36 % -- Input Database Coverage: 10027411 bp out of 45367990 bp ( 22.10 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 440391 Comparison Time: 00:09:52 (hh:mm:ss) Elapsed Time, 2860 HSPs Collected Number of families returned by RECON: 875 Round Time: 00:14:05 (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 : 00:00:03 (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... 3094 repeats masked totaling 754676 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005368 bp Num Contigs Represented = 2650 Non ambiguous bp: Initial: 30000574 bp After Masking: 29194917 bp Masked: 2.69 % -- Input Database Coverage: 40032779 bp out of 45367990 bp ( 88.24 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3946645 Comparison Time: 00:43:24 (hh:mm:ss) Elapsed Time, 21276 HSPs Collected Number of families returned by RECON: 4171 Round Time: 00:47:39 (hh:mm:ss) Elapsed Time : 18 families discovered. - Increasing sample size to include end piece now = 95340579 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 95340579 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 600 repeats masked totaling 127041 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 5335031 bp Num Contigs Represented = 443 Non ambiguous bp: Initial: 5334156 bp After Masking: 5200119 bp Masked: 2.51 % -- Input Database Coverage: 45367810 bp out of 45367990 bp ( 100.00 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 100128 Comparison Time: 00:04:17 (hh:mm:ss) Elapsed Time, 567 HSPs Collected Number of families returned by RECON: 327 Round Time: 00:04:41 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 104 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.GltrIi/RM_3729401.WedSep100128472025 # 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: 00:00:40 (hh:mm:ss) Elapsed Time Program Time: 01:09:15 (hh:mm:ss) Elapsed Time