RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.x22QrJ/RM_2211693.WedJun171734382026 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: 1781742877 Database = /dev/shm/rModeler.x22QrJ/GCF_964273705.1_rNatHel1.hap1.1 - Sequences = 487 - Bases = 1777516490 - N50 = 298881593 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 351695050-376816054 | [ 1 ] 326574046-351695049 | [ ] 301453043-326574046 | [ ] 276332039-301453042 | [ 1 ] 251211036-276332039 | [ ] 226090032-251211035 | [ ] 200969028-226090031 | [ ] 175848025-200969028 | [ 1 ] 150727021-175848024 | [ 2 ] 125606018-150727021 | [ 1 ] 100485014-125606017 | [ ] 75364010-100485013 | [ 3 ] 50243007-75364010 | [ ] 25122003-50243006 | [ 2 ] 1000-25122003 |************************************************** [ 476 ] Storage Throughput = excellent ( 1531.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033965 bp ( 40026965 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 565 raw families identified - RepeatScout: Running filtering stage.. 494 families remaining - RepeatScout: 00:02:57 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 484 families... 00:08:12 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 4 satellite(s), 197 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:12:43 (hh:mm:ss) Elapsed Time : 283 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14558 repeats masked totaling 3528827 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005484 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10003684 bp After Masking: 5843462 bp Masked: 41.59 % -- Input Database Coverage: 10005484 bp out of 1777516490 bp ( 0.56 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:26 (hh:mm:ss) Elapsed Time, 122931 HSPs Collected Number of families returned by RECON: 1266 Round Time: 00:05:41 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48821 repeats masked totaling 12107976 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028401 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30023201 bp After Masking: 15850218 bp Masked: 47.21 % -- Input Database Coverage: 40033885 bp out of 1777516490 bp ( 2.25 % ) Sampling Time: 00:03:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:31 (hh:mm:ss) Elapsed Time, 87062 HSPs Collected Number of families returned by RECON: 2922 Round Time: 00:17:40 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 160863 repeats masked totaling 38026906 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90061029 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90038344 bp After Masking: 45814482 bp Masked: 49.12 % -- Input Database Coverage: 130094914 bp out of 1777516490 bp ( 7.32 % ) Sampling Time: 00:12:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:11:12 (hh:mm:ss) Elapsed Time, 171877 HSPs Collected Number of families returned by RECON: 7589 Round Time: 01:25:44 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 544487 repeats masked totaling 126535145 bp(s). - TE Masking time 00:05:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270093121 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270032727 bp After Masking: 128582597 bp Masked: 52.38 % -- Input Database Coverage: 400188035 bp out of 1777516490 bp ( 22.51 % ) Sampling Time: 00:30:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 07:47:07 (hh:mm:ss) Elapsed Time, 407750 HSPs Collected Number of families returned by RECON: 24270 Round Time: 08:28:28 (hh:mm:ss) Elapsed Time : 693 families discovered. RepeatScout/RECON discovery complete: 1380 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.x22QrJ/RM_2211693.WedJun171734382026 # 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: 00:03:11 (hh:mm:ss) Elapsed Time Program Time: 10:33:27 (hh:mm:ss) Elapsed Time