RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.cDWvZw/RM_3190609.TueSep90315452025 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: 1757412945 Database = /dev/shm/rModeler.cDWvZw/GCA_003946985.1_NRRL62584.SPAdes - Sequences = 1006 - Bases = 47520037 - N50 = 169639 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 760311-814548 | [ 3 ] 706074-760310 | [ ] 651838-706074 | [ ] 597601-651837 | [ ] 543365-597601 | [ 1 ] 489128-543364 | [ 3 ] 434892-489128 | [ 3 ] 380655-434891 | [ 1 ] 326419-380655 | [ 12 ] 272182-326418 | [ 15 ] 217946-272182 | [ 13 ] 163709-217945 |** [ 36 ] 109473-163709 |*** [ 51 ] 55236-109472 |****** [ 100 ] 1000-55236 |************************************************** [ 768 ] Storage Throughput = excellent ( 1659.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022723 bp ( 40021388 non ambiguous ) - Num Contigs Represented = 896 - 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.. : 61 raw families identified - RepeatScout: Running filtering stage.. 33 families remaining - RepeatScout: 00:00:44 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 30 families... 00:00:05 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 8 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465 repeats masked totaling 63829 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006476 bp Num Contigs Represented = 303 Non ambiguous bp: Initial: 10006476 bp After Masking: 9930330 bp Masked: 0.76 % -- Input Database Coverage: 10006476 bp out of 47520037 bp ( 21.06 % ) Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 82215 Comparison Time: 00:04:49 (hh:mm:ss) Elapsed Time, 2576 HSPs Collected Number of families returned by RECON: 858 Round Time: 00:05:04 (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 : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1885 repeats masked totaling 214643 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016167 bp Num Contigs Represented = 739 Non ambiguous bp: Initial: 30014832 bp After Masking: 29768490 bp Masked: 0.82 % -- Input Database Coverage: 40022643 bp out of 47520037 bp ( 84.22 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 730236 Comparison Time: 00:22:22 (hh:mm:ss) Elapsed Time, 18701 HSPs Collected Number of families returned by RECON: 3902 Round Time: 00:24:44 (hh:mm:ss) Elapsed Time : 22 families discovered. - Increasing sample size to include end piece now = 97513561 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 97513561 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... 590 repeats masked totaling 86257 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 7497180 bp Num Contigs Represented = 246 Non ambiguous bp: Initial: 7496875 bp After Masking: 7402725 bp Masked: 1.26 % -- Input Database Coverage: 47519823 bp out of 47520037 bp ( 100.00 % ) Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 44850 Comparison Time: 00:03:42 (hh:mm:ss) Elapsed Time, 918 HSPs Collected Number of families returned by RECON: 430 Round Time: 00:03:59 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 46 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.cDWvZw/RM_3190609.TueSep90315452025 # 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: 00:00:09 (hh:mm:ss) Elapsed Time Program Time: 00:34:50 (hh:mm:ss) Elapsed Time