RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.bWaYVO/RM_1876795.ThuSep41252562025 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: 1757015575 Database = /dev/shm/rModeler.bWaYVO/GCA_040954595.2_keBalMisa1.hap2 - Sequences = 72 - Bases = 319515952 Storage Throughput = excellent ( 1093.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036895 bp ( 40034795 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 520 raw families identified - RepeatScout: Running filtering stage.. 447 families remaining - RepeatScout: 00:09:06 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 429 families... 01:24:41 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 30 satellite(s), 144 contained, found in 00:00:26 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:26 (hh:mm:ss) Elapsed Time Round Time: 01:34:38 (hh:mm:ss) Elapsed Time : 258 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6628 repeats masked totaling 1466403 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040141 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10039641 bp After Masking: 7505515 bp Masked: 25.24 % -- Input Database Coverage: 10040141 bp out of 319515952 bp ( 3.14 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 8009 HSPs Collected Number of families returned by RECON: 802 Round Time: 00:07:06 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21665 repeats masked totaling 5049351 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036676 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30035076 bp After Masking: 21925936 bp Masked: 27.00 % -- Input Database Coverage: 40076817 bp out of 319515952 bp ( 12.54 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:28:21 (hh:mm:ss) Elapsed Time, 41434 HSPs Collected Number of families returned by RECON: 2973 Round Time: 00:35:51 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66688 repeats masked totaling 15208113 bp(s). - TE Masking time 00:04:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038712 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90031486 bp After Masking: 65795672 bp Masked: 26.92 % -- Input Database Coverage: 130115529 bp out of 319515952 bp ( 40.72 % ) Sampling Time: 00:21:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:18:30 (hh:mm:ss) Elapsed Time, 269367 HSPs Collected Number of families returned by RECON: 10502 Round Time: 03:51:27 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 175147 repeats masked totaling 43591470 bp(s). - TE Masking time 00:21:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 189400130 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 189384956 bp After Masking: 125627352 bp Masked: 33.67 % -- Input Database Coverage: 319515659 bp out of 319515952 bp ( 100.00 % ) Sampling Time: 00:46:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11283625 Comparison Time: 12:12:30 (hh:mm:ss) Elapsed Time, 491334 HSPs Collected Number of families returned by RECON: 21600 Round Time: 13:22:17 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatScout/RECON discovery complete: 1002 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.bWaYVO/RM_1876795.ThuSep41252562025 # 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: 00:15:02 (hh:mm:ss) Elapsed Time Program Time: 19:46:21 (hh:mm:ss) Elapsed Time