RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.rHKE5h/RM_2154358.ThuSep41214582025 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: 1757013298 Database = /dev/shm/rModeler.rHKE5h/GCA_013358815.1_fEleEle1.pri - Sequences = 90 - Bases = 589376265 Storage Throughput = excellent ( 1163.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41000264 bp ( 40036118 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 257 raw families identified - RepeatScout: Running filtering stage.. 224 families remaining - RepeatScout: 00:13:57 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 214 families... 00:11:14 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 12 satellite(s), 78 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 00:25:54 (hh:mm:ss) Elapsed Time : 124 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 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3586 repeats masked totaling 741732 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10336630 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10005168 bp After Masking: 8144549 bp Masked: 18.60 % -- Input Database Coverage: 10336630 bp out of 589376265 bp ( 1.75 % ) Sampling Time: 00:02:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:54 (hh:mm:ss) Elapsed Time, 4718 HSPs Collected Number of families returned by RECON: 874 Round Time: 00:09:36 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11841 repeats masked totaling 2561054 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30663554 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30030870 bp After Masking: 24704606 bp Masked: 17.74 % -- Input Database Coverage: 41000184 bp out of 589376265 bp ( 6.96 % ) Sampling Time: 00:09:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:33:42 (hh:mm:ss) Elapsed Time, 37449 HSPs Collected Number of families returned by RECON: 3411 Round Time: 00:43:50 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48478 repeats masked totaling 9180116 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91867145 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90018888 bp After Masking: 72208249 bp Masked: 19.79 % -- Input Database Coverage: 132867329 bp out of 589376265 bp ( 22.54 % ) Sampling Time: 00:24:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2650753 Comparison Time: 04:03:41 (hh:mm:ss) Elapsed Time, 141931 HSPs Collected Number of families returned by RECON: 13364 Round Time: 04:35:56 (hh:mm:ss) Elapsed Time : 244 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 200842 repeats masked totaling 37022745 bp(s). - TE Masking time 00:12:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274934789 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 270032260 bp After Masking: 207189282 bp Masked: 23.27 % -- Input Database Coverage: 407802118 bp out of 589376265 bp ( 69.19 % ) Sampling Time: 01:24:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23760171 Comparison Time: 31:49:21 (hh:mm:ss) Elapsed Time, 460392 HSPs Collected Number of families returned by RECON: 54898 Round Time: 34:30:49 (hh:mm:ss) Elapsed Time : 712 families discovered. RepeatScout/RECON discovery complete: 1157 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.rHKE5h/RM_2154358.ThuSep41214582025 # 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: 00:08:20 (hh:mm:ss) Elapsed Time Program Time: 40:34:25 (hh:mm:ss) Elapsed Time