RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.m2ygWC/RM_247997.WedJan71406472026 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: 1767823607 Database = /dev/shm/rModeler.m2ygWC/GCA_052327205.1_FLI_Smic_1.0 - Sequences = 2112 - Bases = 6448622878 - N50 = 253238922 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 433616002-464588503 | [ 1 ] 402643502-433616002 | [ ] 371671002-402643502 | [ 2 ] 340698502-371671002 | [ 1 ] 309726002-340698502 | [ 1 ] 278753501-309726001 | [ 2 ] 247781001-278753501 | [ 2 ] 216808501-247781001 | [ 3 ] 185836001-216808501 | [ 1 ] 154863501-185836001 | [ 1 ] 123891000-154863500 | [ 2 ] 92918500-123891000 | [ 3 ] 61946000-92918500 | [ 8 ] 30973500-61946000 | [ 15 ] 1000-30973500 |************************************************** [ 2070 ] Storage Throughput = excellent ( 1538.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40051510 bp ( 40013125 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 568 raw families identified - RepeatScout: Running filtering stage.. 400 families remaining - RepeatScout: 00:07:53 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 394 families... 00:05:14 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 4 satellite(s), 137 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time Round Time: 00:14:54 (hh:mm:ss) Elapsed Time : 254 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11022 repeats masked totaling 5821113 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031779 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10024779 bp After Masking: 2070224 bp Masked: 79.35 % -- Input Database Coverage: 10031779 bp out of 6448622878 bp ( 0.16 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:43 (hh:mm:ss) Elapsed Time, 8727 HSPs Collected Number of families returned by RECON: 594 Round Time: 00:07:37 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34305 repeats masked totaling 17832044 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30059651 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30028266 bp After Masking: 6159707 bp Masked: 79.49 % -- Input Database Coverage: 40091430 bp out of 6448622878 bp ( 0.62 % ) Sampling Time: 00:12:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:09:28 (hh:mm:ss) Elapsed Time, 19474 HSPs Collected Number of families returned by RECON: 1697 Round Time: 00:22:10 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110685 repeats masked totaling 53935657 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90097911 bp Num Contigs Represented = 176 Non ambiguous bp: Initial: 90007943 bp After Masking: 17248624 bp Masked: 80.84 % -- Input Database Coverage: 130189341 bp out of 6448622878 bp ( 2.02 % ) Sampling Time: 00:43:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 00:37:00 (hh:mm:ss) Elapsed Time, 104531 HSPs Collected Number of families returned by RECON: 4504 Round Time: 01:22:14 (hh:mm:ss) Elapsed Time : 224 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:43:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 379503 repeats masked totaling 171651738 bp(s). - TE Masking time 00:05:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270259749 bp Num Contigs Represented = 394 Non ambiguous bp: Initial: 270014808 bp After Masking: 44834528 bp Masked: 83.40 % -- Input Database Coverage: 400449090 bp out of 6448622878 bp ( 6.21 % ) Sampling Time: 02:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 03:00:03 (hh:mm:ss) Elapsed Time, 262872 HSPs Collected Number of families returned by RECON: 10607 Round Time: 05:05:17 (hh:mm:ss) Elapsed Time : 450 families discovered. RepeatScout/RECON discovery complete: 986 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.m2ygWC/RM_247997.WedJan71406472026 # 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: 00:03:05 (hh:mm:ss) Elapsed Time Program Time: 07:15:17 (hh:mm:ss) Elapsed Time