RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.ZRSKlQ/RM_3145225.SatSep130509462025 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: 1757765385 Database = /dev/shm/rModeler.ZRSKlQ/GCA_030280995.1_Hv_R1_Cat_CENPAT - Sequences = 794 - Bases = 747980110 - N50 = 36646690 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 66654507-71415227 | [ 1 ] 61893788-66654507 | [ ] 57133068-61893787 | [ ] 52372349-57133068 | [ 1 ] 47611629-52372348 | [ 1 ] 42850910-47611629 | [ 1 ] 38090190-42850909 | [ 1 ] 33329471-38090190 | [ 5 ] 28568751-33329470 | [ 5 ] 23808032-28568751 | [ 3 ] 19047312-23808031 | [ ] 14286593-19047312 | [ ] 9525873-14286592 | [ 1 ] 4765154-9525873 | [ 1 ] 4435-4765154 |************************************************** [ 774 ] Storage Throughput = excellent ( 1094.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032603 bp ( 40032603 non ambiguous ) - Num Contigs Represented = 94 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 283 raw families identified - RepeatScout: Running filtering stage.. 255 families remaining - RepeatScout: 00:16:48 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 255 families... 01:06:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 21 satellite(s), 73 contained, found in 00:00:27 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:28 (hh:mm:ss) Elapsed Time Round Time: 01:24:12 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (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... 8838 repeats masked totaling 7223650 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006898 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10006898 bp After Masking: 2622834 bp Masked: 73.79 % -- Input Database Coverage: 10006898 bp out of 747980110 bp ( 1.34 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 91481 HSPs Collected Number of families returned by RECON: 351 Round Time: 00:14:13 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22622 repeats masked totaling 24497344 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025698 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30025698 bp After Masking: 5058949 bp Masked: 83.15 % -- Input Database Coverage: 40032596 bp out of 747980110 bp ( 5.35 % ) Sampling Time: 00:07:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:14:21 (hh:mm:ss) Elapsed Time, 18133 HSPs Collected Number of families returned by RECON: 908 Round Time: 00:22:38 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68246 repeats masked totaling 74350058 bp(s). - TE Masking time 00:11:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030704 bp Num Contigs Represented = 194 Non ambiguous bp: Initial: 90030404 bp After Masking: 14194469 bp Masked: 84.23 % -- Input Database Coverage: 130063300 bp out of 747980110 bp ( 17.39 % ) Sampling Time: 00:24:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 01:16:06 (hh:mm:ss) Elapsed Time, 187148 HSPs Collected Number of families returned by RECON: 2544 Round Time: 01:45:19 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 216585 repeats masked totaling 232427531 bp(s). - TE Masking time 00:55:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009114 bp Num Contigs Represented = 449 Non ambiguous bp: Initial: 270008420 bp After Masking: 33287687 bp Masked: 87.67 % -- Input Database Coverage: 400072414 bp out of 747980110 bp ( 53.49 % ) Sampling Time: 01:32:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23698170 Comparison Time: 06:19:33 (hh:mm:ss) Elapsed Time, 533115 HSPs Collected Number of families returned by RECON: 7328 Round Time: 30:16:09 (hh:mm:ss) Elapsed Time : 226 families discovered. RepeatScout/RECON discovery complete: 571 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.ZRSKlQ/RM_3145225.SatSep130509462025 # 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: 00:08:17 (hh:mm:ss) Elapsed Time Program Time: 34:10:48 (hh:mm:ss) Elapsed Time