RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.t8woSb/RM_310633.WedSep31057452025 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: 1756922264 Database = /dev/shm/rModeler.t8woSb/GCA_042242115.1_fArrGeo1.hap1 - Sequences = 625 - Bases = 735099811 - N50 = 29028568 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32899420-35249078 | [ 1 ] 30549762-32899419 | [ 5 ] 28200104-30549761 | [ 7 ] 25850446-28200103 | [ 5 ] 23500788-25850445 | [ 2 ] 21151130-23500787 | [ 1 ] 18801472-21151129 | [ 2 ] 16451815-18801472 | [ ] 14102157-16451814 | [ 1 ] 11752499-14102156 | [ ] 9402841-11752498 | [ ] 7053183-9402840 | [ ] 4703525-7053182 | [ ] 2353867-4703524 | [ ] 4210-2353867 |************************************************** [ 601 ] Storage Throughput = excellent ( 1093.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019248 bp ( 40018448 non ambiguous ) - Num Contigs Represented = 115 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 218 raw families identified - RepeatScout: Running filtering stage.. 196 families remaining - RepeatScout: 00:08:32 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 183 families... 00:43:03 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 13 satellite(s), 51 contained, found in 00:00:11 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:12 (hh:mm:ss) Elapsed Time Round Time: 00:52:24 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3888 repeats masked totaling 597033 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032046 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10031646 bp After Masking: 8827590 bp Masked: 12.00 % -- Input Database Coverage: 10032046 bp out of 735099811 bp ( 1.36 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 60756 HSPs Collected Number of families returned by RECON: 1854 Round Time: 00:21:42 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20373 repeats masked totaling 4050633 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027202 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 30026802 bp After Masking: 24680195 bp Masked: 17.81 % -- Input Database Coverage: 40059248 bp out of 735099811 bp ( 5.45 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:36:55 (hh:mm:ss) Elapsed Time, 98893 HSPs Collected Number of families returned by RECON: 5590 Round Time: 00:52:45 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75135 repeats masked totaling 15615347 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030068 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 90027868 bp After Masking: 70310072 bp Masked: 21.90 % -- Input Database Coverage: 130089316 bp out of 735099811 bp ( 17.70 % ) Sampling Time: 00:09:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 04:22:07 (hh:mm:ss) Elapsed Time, 994327 HSPs Collected Number of families returned by RECON: 19121 Round Time: 05:27:12 (hh:mm:ss) Elapsed Time : 400 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 322628 repeats masked totaling 67513325 bp(s). - TE Masking time 00:15:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022621 bp Num Contigs Represented = 415 Non ambiguous bp: Initial: 270014621 bp After Masking: 188737057 bp Masked: 30.10 % -- Input Database Coverage: 400111937 bp out of 735099811 bp ( 54.43 % ) Sampling Time: 00:40:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23471526 Comparison Time: 31:20:10 (hh:mm:ss) Elapsed Time, 672728 HSPs Collected Number of families returned by RECON: 61283 Round Time: 33:42:27 (hh:mm:ss) Elapsed Time : 1012 families discovered. RepeatScout/RECON discovery complete: 1673 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.t8woSb/RM_310633.WedSep31057452025 # 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: 00:07:59 (hh:mm:ss) Elapsed Time Program Time: 41:24:29 (hh:mm:ss) Elapsed Time