RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.VWuviw/RM_1222895.MonSep81603282025 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: 1757372607 Database = /dev/shm/rModeler.VWuviw/GCA_001717905.1_ASM171790v1 - Sequences = 303 - Bases = 36666367 - N50 = 401010 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1200825-1286584 | [ 1 ] 1115067-1200825 | [ ] 1029309-1115067 | [ 3 ] 943551-1029309 | [ 1 ] 857793-943551 | [ ] 772034-857792 | [ 3 ] 686276-772034 | [ ] 600518-686276 | [ 3 ] 514760-600518 |* [ 6 ] 429002-514760 |* [ 6 ] 343243-429001 |*** [ 13 ] 257485-343243 |* [ 7 ] 171727-257485 |****** [ 24 ] 85969-171727 |********** [ 41 ] 211-85969 |************************************************** [ 195 ] Storage Throughput = excellent ( 1651.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 36666297 bp ( 36657180 non ambiguous ) - Num Contigs Represented = 303 - 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.. : 14 raw families identified - RepeatScout: Running filtering stage.. 14 families remaining - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 11 families... 00:00:04 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:44 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153 repeats masked totaling 16745 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032505 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 10030301 bp After Masking: 10000873 bp Masked: 0.29 % -- Input Database Coverage: 10032505 bp out of 36666367 bp ( 27.36 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 49455 Comparison Time: 00:04:00 (hh:mm:ss) Elapsed Time, 31165 HSPs Collected Number of families returned by RECON: 896 Round Time: 00:04:17 (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 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 495 repeats masked totaling 54541 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 26633772 bp Num Contigs Represented = 254 Non ambiguous bp: Initial: 26626859 bp After Masking: 26543985 bp Masked: 0.31 % -- Input Database Coverage: 36666277 bp out of 36666367 bp ( 100.00 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 324415 Comparison Time: 00:14:04 (hh:mm:ss) Elapsed Time, 179757 HSPs Collected Number of families returned by RECON: 3334 Round Time: 00:14:55 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatScout/RECON discovery complete: 20 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.VWuviw/RM_1222895.MonSep81603282025 # 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: 00:00:06 (hh:mm:ss) Elapsed Time Program Time: 00:20:02 (hh:mm:ss) Elapsed Time