RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.mbOLgX/RM_2690189.FriSep122231432025 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: 1757741503 Database = /dev/shm/rModeler.mbOLgX/GCA_051943735.1_ASM5194373v1 - Sequences = 2304 - Bases = 23245542 - N50 = 49724 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188213-201643 | [ 2 ] 174783-188212 | [ 1 ] 161354-174783 | [ 4 ] 147924-161353 | [ 3 ] 134495-147924 | [ 3 ] 121065-134494 | [ 5 ] 107636-121065 | [ 7 ] 94206-107635 | [ 19 ] 80777-94206 | [ 10 ] 67347-80776 | [ 21 ] 53918-67347 |* [ 42 ] 40488-53917 |* [ 74 ] 27059-40488 |** [ 105 ] 13629-27058 |**** [ 157 ] 200-13629 |************************************************* [ 1851 ] Storage Throughput = excellent ( 1705.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 23245422 bp ( 23242088 non ambiguous ) - Num Contigs Represented = 2304 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 37 raw families identified - RepeatScout: Running filtering stage.. 37 families remaining - RepeatScout: 00:00:28 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 36 families... 00:00:11 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 7 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:42 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (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... 939 repeats masked totaling 365376 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031361 bp Num Contigs Represented = 1076 Non ambiguous bp: Initial: 10030158 bp After Masking: 9626271 bp Masked: 4.03 % -- Input Database Coverage: 10031361 bp out of 23245542 bp ( 43.15 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 648091 Comparison Time: 00:06:32 (hh:mm:ss) Elapsed Time, 2054 HSPs Collected Number of families returned by RECON: 641 Round Time: 00:06:50 (hh:mm:ss) Elapsed Time : 4 families discovered. - Increasing sample size to include end piece now = 43245542 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 43245542 bp - Sequence extraction : 00:00:00 (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... 1172 repeats masked totaling 400682 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 13213981 bp Num Contigs Represented = 1344 Non ambiguous bp: Initial: 13211850 bp After Masking: 12753978 bp Masked: 3.47 % -- Input Database Coverage: 23245342 bp out of 23245542 bp ( 100.00 % ) Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1037520 Comparison Time: 00:08:47 (hh:mm:ss) Elapsed Time, 2949 HSPs Collected Number of families returned by RECON: 1006 Round Time: 00:09:12 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatScout/RECON discovery complete: 38 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.mbOLgX/RM_2690189.FriSep122231432025 # 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: 00:16:53 (hh:mm:ss) Elapsed Time