RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Ggi2LY/RM_3138416.ThuSep41254142025 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: 1757015653 Database = /dev/shm/rModeler.Ggi2LY/GCA_043640875.1_fEnoArm2.hap2 - Sequences = 94 - Bases = 578326983 Storage Throughput = excellent ( 1168.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010507 bp ( 40009407 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 163 raw families identified - RepeatScout: Running filtering stage.. 151 families remaining - RepeatScout: 00:04:07 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 139 families... 00:15:31 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 3 satellite(s), 40 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:20:15 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3680 repeats masked totaling 576180 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009174 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10009174 bp After Masking: 9160175 bp Masked: 8.48 % -- Input Database Coverage: 10009174 bp out of 578326983 bp ( 1.73 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 67053 HSPs Collected Number of families returned by RECON: 1939 Round Time: 00:08:09 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16173 repeats masked totaling 2537247 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001304 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30000204 bp After Masking: 26827105 bp Masked: 10.58 % -- Input Database Coverage: 40010478 bp out of 578326983 bp ( 6.92 % ) Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:37:35 (hh:mm:ss) Elapsed Time, 70802 HSPs Collected Number of families returned by RECON: 5969 Round Time: 00:41:35 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72288 repeats masked totaling 10370077 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019390 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90014990 bp After Masking: 77780763 bp Masked: 13.59 % -- Input Database Coverage: 130029868 bp out of 578326983 bp ( 22.48 % ) Sampling Time: 00:07:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 04:36:15 (hh:mm:ss) Elapsed Time, 297008 HSPs Collected Number of families returned by RECON: 22366 Round Time: 04:59:07 (hh:mm:ss) Elapsed Time : 374 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 316671 repeats masked totaling 42492507 bp(s). - TE Masking time 00:09:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034178 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 270025978 bp After Masking: 222091501 bp Masked: 17.75 % -- Input Database Coverage: 400064046 bp out of 578326983 bp ( 69.18 % ) Sampling Time: 00:27:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 35:25:55 (hh:mm:ss) Elapsed Time, 682418 HSPs Collected Number of families returned by RECON: 76422 Round Time: 38:15:41 (hh:mm:ss) Elapsed Time : 917 families discovered. RepeatScout/RECON discovery complete: 1515 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Ggi2LY/RM_3138416.ThuSep41254142025 # 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: 00:05:36 (hh:mm:ss) Elapsed Time Program Time: 44:30:23 (hh:mm:ss) Elapsed Time