RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.1YpcVa/RM_763925.TueSep90553142025 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: 1757422393 Database = /dev/shm/rModeler.1YpcVa/GCA_009663055.1_ASM966305v1 - Sequences = 12 - Bases = 43722320 Storage Throughput = excellent ( 1611.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40048958 bp ( 40029595 non ambiguous ) - Num Contigs Represented = 12 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 34 raw families identified - RepeatScout: Running filtering stage.. 31 families remaining - RepeatScout: 00:00:52 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 31 families... 01:08:58 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 4 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 01:10:00 (hh:mm:ss) Elapsed Time : 26 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 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 316 repeats masked totaling 355980 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022222 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10020915 bp After Masking: 9655816 bp Masked: 3.64 % -- Input Database Coverage: 10022222 bp out of 43722320 bp ( 22.92 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:36 (hh:mm:ss) Elapsed Time, 13269 HSPs Collected Number of families returned by RECON: 705 Round Time: 00:04:45 (hh:mm:ss) Elapsed Time : 3 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 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1318 repeats masked totaling 1407434 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026667 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 30008611 bp After Masking: 28570249 bp Masked: 4.79 % -- Input Database Coverage: 40048889 bp out of 43722320 bp ( 91.60 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:16:43 (hh:mm:ss) Elapsed Time, 125304 HSPs Collected Number of families returned by RECON: 3632 Round Time: 00:33:50 (hh:mm:ss) Elapsed Time : 9 families discovered. - Increasing sample size to include end piece now = 93700098 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 93700098 bp - Sequence extraction : 00:00:00 (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... 219 repeats masked totaling 221945 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3673145 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 3671774 bp After Masking: 3446800 bp Masked: 6.13 % -- Input Database Coverage: 43722034 bp out of 43722320 bp ( 100.00 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4278 Comparison Time: 00:01:05 (hh:mm:ss) Elapsed Time, 1864 HSPs Collected Number of families returned by RECON: 112 Round Time: 00:02:47 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 39 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.1YpcVa/RM_763925.TueSep90553142025 # 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: 00:00:20 (hh:mm:ss) Elapsed Time Program Time: 01:51:42 (hh:mm:ss) Elapsed Time