RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Y3CNmQ/RM_1513658.FriSep120424142025 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: 1757676253 Database = /dev/shm/rModeler.Y3CNmQ/GCA_034769205.1_ASM3476920v1 - Sequences = 183 - Bases = 60173375 - N50 = 1419924 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 5224779-5597958 | [ 1 ] 4851601-5224779 | [ ] 4478423-4851601 | [ ] 4105244-4478422 | [ ] 3732066-4105244 | [ ] 3358888-3732066 | [ 1 ] 2985710-3358888 | [ 1 ] 2612531-2985709 | [ ] 2239353-2612531 |* [ 4 ] 1866175-2239353 | [ 1 ] 1492997-1866175 | [ 2 ] 1119818-1492996 |* [ 4 ] 746640-1119818 |**** [ 12 ] 373462-746640 |****** [ 19 ] 284-373462 |************************************************** [ 138 ] Storage Throughput = excellent ( 1723.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007676 bp ( 40007676 non ambiguous ) - Num Contigs Represented = 153 - 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.. : 577 raw families identified - RepeatScout: Running filtering stage.. 562 families remaining - RepeatScout: 00:04:07 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 554 families... 00:02:42 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 207 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 00:06:59 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7677 repeats masked totaling 3664156 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036877 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 10036877 bp After Masking: 6292677 bp Masked: 37.30 % -- Input Database Coverage: 10036877 bp out of 60173375 bp ( 16.68 % ) Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 39340 Comparison Time: 00:03:39 (hh:mm:ss) Elapsed Time, 8721 HSPs Collected Number of families returned by RECON: 785 Round Time: 00:04:34 (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 : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22220 repeats masked totaling 11110881 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010719 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 30010719 bp After Masking: 18613534 bp Masked: 37.98 % -- Input Database Coverage: 40047596 bp out of 60173375 bp ( 66.55 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 327645 Comparison Time: 00:13:33 (hh:mm:ss) Elapsed Time, 40427 HSPs Collected Number of families returned by RECON: 3010 Round Time: 00:16:22 (hh:mm:ss) Elapsed Time : 34 families discovered. - Increasing sample size to include end piece now = 110136498 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 110136498 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15020 repeats masked totaling 7456682 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 20125538 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 20125428 bp After Masking: 12549806 bp Masked: 37.64 % -- Input Database Coverage: 60173134 bp out of 60173375 bp ( 100.00 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 144991 Comparison Time: 00:08:15 (hh:mm:ss) Elapsed Time, 9230 HSPs Collected Number of families returned by RECON: 1821 Round Time: 00:09:24 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatScout/RECON discovery complete: 400 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Y3CNmQ/RM_1513658.FriSep120424142025 # 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: 00:01:01 (hh:mm:ss) Elapsed Time Program Time: 00:38:20 (hh:mm:ss) Elapsed Time