RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.gEIF2v/RM_304894.ThuOct301621542025 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: 1761866513 Database = /dev/shm/rModeler.gEIF2v/GCA_026008535.1_Pfru_yukari_1.0 - Sequences = 71 - Bases = 1258994547 Storage Throughput = excellent ( 1183.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036943 bp ( 40036443 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 829 raw families identified - RepeatScout: Running filtering stage.. 693 families remaining - RepeatScout: 00:09:03 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 687 families... 02:22:26 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 6 satellite(s), 242 contained, found in 00:00:19 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:20 (hh:mm:ss) Elapsed Time Round Time: 02:32:49 (hh:mm:ss) Elapsed Time : 438 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (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... 9701 repeats masked totaling 4974026 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000818 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000818 bp After Masking: 4674591 bp Masked: 53.26 % -- Input Database Coverage: 10000818 bp out of 1258994547 bp ( 0.79 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:26 (hh:mm:ss) Elapsed Time, 14901 HSPs Collected Number of families returned by RECON: 1467 Round Time: 00:07:47 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30862 repeats masked totaling 15290293 bp(s). - TE Masking time 00:03:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036045 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30035545 bp After Masking: 13999824 bp Masked: 53.39 % -- Input Database Coverage: 40036863 bp out of 1258994547 bp ( 3.18 % ) Sampling Time: 00:06:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:28:13 (hh:mm:ss) Elapsed Time, 65632 HSPs Collected Number of families returned by RECON: 4451 Round Time: 00:36:17 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105838 repeats masked totaling 50080054 bp(s). - TE Masking time 00:13:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033833 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90033333 bp After Masking: 37767470 bp Masked: 58.05 % -- Input Database Coverage: 130070696 bp out of 1258994547 bp ( 10.33 % ) Sampling Time: 00:19:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:48:59 (hh:mm:ss) Elapsed Time, 316117 HSPs Collected Number of families returned by RECON: 12622 Round Time: 03:22:35 (hh:mm:ss) Elapsed Time : 357 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358646 repeats masked totaling 167718954 bp(s). - TE Masking time 01:14:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041896 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270039396 bp After Masking: 95220544 bp Masked: 64.74 % -- Input Database Coverage: 400112592 bp out of 1258994547 bp ( 31.78 % ) Sampling Time: 01:37:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 17:28:21 (hh:mm:ss) Elapsed Time, 1062642 HSPs Collected Number of families returned by RECON: 34949 Round Time: 20:06:26 (hh:mm:ss) Elapsed Time : 893 families discovered. RepeatScout/RECON discovery complete: 1814 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.gEIF2v/RM_304894.ThuOct301621542025 # 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: 00:20:46 (hh:mm:ss) Elapsed Time Program Time: 27:06:40 (hh:mm:ss) Elapsed Time