RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.ZFH16w/RM_764048.TueSep90553162025 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: 1757422395 Database = /dev/shm/rModeler.ZFH16w/GCA_009663095.1_ASM966309v1 - Sequences = 12 - Bases = 43737213 Storage Throughput = excellent ( 1629.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40049760 bp ( 40028896 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.. : 39 raw families identified - RepeatScout: Running filtering stage.. 35 families remaining - RepeatScout: 00:00:52 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 33 families... 01:39:03 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:08 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:08 (hh:mm:ss) Elapsed Time Round Time: 01:40:08 (hh:mm:ss) Elapsed Time : 33 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 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 632 repeats masked totaling 557937 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029383 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10027467 bp After Masking: 9458599 bp Masked: 5.67 % -- Input Database Coverage: 10029383 bp out of 43737213 bp ( 22.93 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:46 (hh:mm:ss) Elapsed Time, 2418 HSPs Collected Number of families returned by RECON: 559 Round Time: 00:21:36 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2071 repeats masked totaling 1464225 bp(s). - TE Masking time 00:03:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020297 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 30001349 bp After Masking: 28508383 bp Masked: 4.98 % -- Input Database Coverage: 40049680 bp out of 43737213 bp ( 91.57 % ) Sampling Time: 00:03:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:14:41 (hh:mm:ss) Elapsed Time, 10892 HSPs Collected Number of families returned by RECON: 3207 Round Time: 00:19:15 (hh:mm:ss) Elapsed Time : 4 families discovered. - Increasing sample size to include end piece now = 93707830 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 93707830 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... 277 repeats masked totaling 252036 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3687316 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 3686412 bp After Masking: 3431390 bp Masked: 6.92 % -- Input Database Coverage: 43736996 bp out of 43737213 bp ( 100.00 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4186 Comparison Time: 00:01:07 (hh:mm:ss) Elapsed Time, 136 HSPs Collected Number of families returned by RECON: 106 Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 42 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.ZFH16w/RM_764048.TueSep90553162025 # 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: 00:00:27 (hh:mm:ss) Elapsed Time Program Time: 02:25:14 (hh:mm:ss) Elapsed Time