RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.YzfRgl/RM_3942433.FriSep122041272025 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: 1757734886 Database = /dev/shm/rModeler.YzfRgl/GCA_051397765.1_GA15_2 - Sequences = 695 - Bases = 40415298 - N50 = 201939 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 650128-696530 | [ 1 ] 603726-650127 | [ 2 ] 557324-603725 | [ 2 ] 510923-557324 | [ 2 ] 464521-510922 | [ 2 ] 418119-464520 | [ 3 ] 371717-418118 | [ 7 ] 325316-371717 | [ 6 ] 278914-325315 |* [ 10 ] 232512-278913 |* [ 11 ] 186110-232511 |** [ 23 ] 139709-186110 |*** [ 30 ] 93307-139708 |***** [ 49 ] 46905-93306 |****** [ 65 ] 504-46905 |************************************************** [ 482 ] Storage Throughput = excellent ( 1654.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030044 bp ( 40028926 non ambiguous ) - Num Contigs Represented = 690 - 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.. : 43 raw families identified - RepeatScout: Running filtering stage.. 41 families remaining - RepeatScout: 00:00:41 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 39 families... 00:00:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 34 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 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 490 repeats masked totaling 133570 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035582 bp Num Contigs Represented = 231 Non ambiguous bp: Initial: 10035349 bp After Masking: 9876806 bp Masked: 1.58 % -- Input Database Coverage: 10035582 bp out of 40415298 bp ( 24.83 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 61776 Comparison Time: 00:04:16 (hh:mm:ss) Elapsed Time, 2017 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:04:31 (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 : 00:00:01 (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... 1277 repeats masked totaling 374600 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038828 bp Num Contigs Represented = 596 Non ambiguous bp: Initial: 30037943 bp After Masking: 29581248 bp Masked: 1.52 % -- Input Database Coverage: 40074410 bp out of 40415298 bp ( 99.16 % ) Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 681528 Comparison Time: 00:17:22 (hh:mm:ss) Elapsed Time, 16810 HSPs Collected Number of families returned by RECON: 4051 Round Time: 00:18:07 (hh:mm:ss) Elapsed Time : 22 families discovered. - Increasing sample size to include end piece now = 90379716 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90379716 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21 repeats masked totaling 4721 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 340677 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 340677 bp After Masking: 335411 bp Masked: 1.55 % -- Input Database Coverage: 40415087 bp out of 40415298 bp ( 100.00 % ) Sampling Time: 00:00:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 78 Comparison Time: 00:00:07 (hh:mm:ss) Elapsed Time, 2 HSPs Collected Round Time: 00:00:09 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 57 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.YzfRgl/RM_3942433.FriSep122041272025 # 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: 00:00:12 (hh:mm:ss) Elapsed Time Program Time: 00:23:53 (hh:mm:ss) Elapsed Time