RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.ivB4f3/RM_2422461.MonSep81624202025 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: 1757373859 Database = /data/tmp/rModeler.ivB4f3/GCA_001931775.1_ASM193177v1 - Sequences = 2178 - Bases = 45982938 - N50 = 105629 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1026851-1100126 | [ 1 ] 953576-1026851 | [ ] 880301-953576 | [ 1 ] 807026-880301 | [ ] 733751-807026 | [ 1 ] 660476-733751 | [ ] 587201-660476 | [ ] 513926-587201 | [ 2 ] 440651-513926 | [ 2 ] 367376-440651 | [ 5 ] 294101-367376 | [ 6 ] 220826-294101 | [ 11 ] 147551-220826 | [ 34 ] 74276-147551 |** [ 86 ] 1001-74276 |************************************************** [ 2029 ] Storage Throughput = excellent ( 1138.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40568383 bp ( 40003088 non ambiguous ) - Num Contigs Represented = 1938 - 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.. : 568 raw families identified - RepeatScout: Running filtering stage.. 563 families remaining - RepeatScout: 00:01:32 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 492 families... 00:01:02 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 117 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:02:42 (hh:mm:ss) Elapsed Time : 374 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 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3108 repeats masked totaling 1220843 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10194977 bp Num Contigs Represented = 584 Non ambiguous bp: Initial: 10033996 bp After Masking: 8786193 bp Masked: 12.44 % -- Input Database Coverage: 10194977 bp out of 45982938 bp ( 22.17 % ) Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 210276 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 3778 HSPs Collected Number of families returned by RECON: 1121 Round Time: 00:06:22 (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 : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9501 repeats masked totaling 3681604 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30413322 bp Num Contigs Represented = 1482 Non ambiguous bp: Initial: 30009007 bp After Masking: 26264934 bp Masked: 12.48 % -- Input Database Coverage: 40608299 bp out of 45982938 bp ( 88.31 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1777555 Comparison Time: 00:29:26 (hh:mm:ss) Elapsed Time, 33120 HSPs Collected Number of families returned by RECON: 4593 Round Time: 00:31:38 (hh:mm:ss) Elapsed Time : 19 families discovered. - Increasing sample size to include end piece now = 95787961 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 95787961 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1992 repeats masked totaling 691242 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 5374372 bp Num Contigs Represented = 329 Non ambiguous bp: Initial: 5296962 bp After Masking: 4596684 bp Masked: 13.22 % -- Input Database Coverage: 45982671 bp out of 45982938 bp ( 100.00 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 63546 Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 1187 HSPs Collected Number of families returned by RECON: 479 Round Time: 00:03:32 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 394 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.ivB4f3/RM_2422461.MonSep81624202025 # 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: 00:01:27 (hh:mm:ss) Elapsed Time Program Time: 00:45:41 (hh:mm:ss) Elapsed Time