RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.0SzM8b/RM_15736.MonSep81318182025 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: 1757362697 Database = /dev/shm/rModeler.0SzM8b/GCA_001023045.1_ASM102304v1 - Sequences = 835 - Bases = 43096072 - N50 = 192288 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 739105-791881 | [ 1 ] 686330-739105 | [ 1 ] 633555-686330 | [ 1 ] 580779-633554 | [ 3 ] 528004-580779 | [ 3 ] 475229-528004 | [ 3 ] 422454-475229 | [ 2 ] 369678-422453 | [ 7 ] 316903-369678 | [ 11 ] 264128-316903 | [ 10 ] 211353-264128 |* [ 14 ] 158577-211352 |* [ 20 ] 105802-158577 |****** [ 77 ] 53027-105802 |***** [ 66 ] 252-53027 |************************************************** [ 616 ] Storage Throughput = excellent ( 1432.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40484630 bp ( 40013517 non ambiguous ) - Num Contigs Represented = 808 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 13 raw families identified - RepeatScout: Running filtering stage.. 13 families remaining - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 12 families... 00:00:06 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time Round Time: 00:00:49 (hh:mm:ss) Elapsed Time : 12 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 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 419 repeats masked totaling 47079 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10124770 bp Num Contigs Represented = 300 Non ambiguous bp: Initial: 10002154 bp After Masking: 9948308 bp Masked: 0.54 % -- Input Database Coverage: 10124770 bp out of 43096072 bp ( 23.49 % ) Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 87571 Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 1571 HSPs Collected Number of families returned by RECON: 639 Round Time: 00:04:42 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1373 repeats masked totaling 148975 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30359831 bp Num Contigs Represented = 657 Non ambiguous bp: Initial: 30011334 bp After Masking: 29841224 bp Masked: 0.57 % -- Input Database Coverage: 40484601 bp out of 43096072 bp ( 93.94 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 746031 Comparison Time: 00:17:50 (hh:mm:ss) Elapsed Time, 11870 HSPs Collected Number of families returned by RECON: 3505 Round Time: 00:18:24 (hh:mm:ss) Elapsed Time : 8 families discovered. - Increasing sample size to include end piece now = 92971302 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 92971302 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132 repeats masked totaling 14509 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2611324 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 2572954 bp After Masking: 2556358 bp Masked: 0.65 % -- Input Database Coverage: 43095925 bp out of 43096072 bp ( 100.00 % ) Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4371 Comparison Time: 00:00:58 (hh:mm:ss) Elapsed Time, 77 HSPs Collected Number of families returned by RECON: 57 Round Time: 00:01:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 22 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.0SzM8b/RM_15736.MonSep81318182025 # 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: 00:00:05 (hh:mm:ss) Elapsed Time Program Time: 00:25:02 (hh:mm:ss) Elapsed Time