RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.X1D4Nd/RM_4057512.MonSep81321572025 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: 1757362917 Database = /dev/shm/rModeler.X1D4Nd/GCA_001023065.1_ASM102306v1 - Sequences = 2959 - Bases = 43499819 - N50 = 27446 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 120295-128850 | [ 2 ] 111741-120295 | [ 1 ] 103187-111741 | [ ] 94632-103186 | [ 3 ] 86078-94632 | [ 8 ] 77524-86078 | [ 11 ] 68970-77524 | [ 18 ] 60415-68969 |* [ 37 ] 51861-60415 |* [ 34 ] 43307-51861 |** [ 73 ] 34753-43307 |**** [ 131 ] 26198-34752 |****** [ 206 ] 17644-26198 |*********** [ 350 ] 9090-17644 |******************** [ 607 ] 536-9090 |************************************************** [ 1478 ] Storage Throughput = excellent ( 1072.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002462 bp ( 40002402 non ambiguous ) - Num Contigs Represented = 2730 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 1 raw families identified - RepeatScout: Running filtering stage.. 1 families remaining - RepeatScout: 00:01:00 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 1 families... 00:00:06 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:16 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 249 repeats masked totaling 27218 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042922 bp Num Contigs Represented = 738 Non ambiguous bp: Initial: 10042902 bp After Masking: 10007150 bp Masked: 0.36 % -- Input Database Coverage: 10042922 bp out of 43499819 bp ( 23.09 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:07:34 (hh:mm:ss) Elapsed Time, 2322 HSPs Collected Number of families returned by RECON: 753 Round Time: 00:07:57 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1456 repeats masked totaling 134072 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002265 bp Num Contigs Represented = 2086 Non ambiguous bp: Initial: 30002225 bp After Masking: 29844411 bp Masked: 0.53 % -- Input Database Coverage: 40045187 bp out of 43499819 bp ( 92.06 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2401336 Comparison Time: 00:36:02 (hh:mm:ss) Elapsed Time, 14655 HSPs Collected Number of families returned by RECON: 3747 Round Time: 00:37:18 (hh:mm:ss) Elapsed Time : 14 families discovered. - Increasing sample size to include end piece now = 93456897 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 93456897 bp - Sequence extraction : 00:00:00 (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... 238 repeats masked totaling 24296 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3454512 bp Num Contigs Represented = 261 Non ambiguous bp: Initial: 3454512 bp After Masking: 3427630 bp Masked: 0.78 % -- Input Database Coverage: 43499699 bp out of 43499819 bp ( 100.00 % ) Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:02:07 (hh:mm:ss) Elapsed Time, 180 HSPs Collected Number of families returned by RECON: 110 Round Time: 00:02:13 (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.X1D4Nd/RM_4057512.MonSep81321572025 # 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: 00:00:11 (hh:mm:ss) Elapsed Time Program Time: 00:48:55 (hh:mm:ss) Elapsed Time