RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.ArhgZB/RM_2259337.FriMar62226362026 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: 1772864795 Database = /dev/shm/rModeler.ArhgZB/GCA_963513985.1_bFriCoe1.1_alternate_haplotype - Sequences = 2178 - Bases = 1168325350 - N50 = 1659831 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 8226422-8813585 | [ 1 ] 7639259-8226421 | [ 1 ] 7052096-7639258 | [ 1 ] 6464933-7052095 | [ 2 ] 5877770-6464932 | [ 4 ] 5290607-5877769 | [ 2 ] 4703444-5290606 | [ 5 ] 4116281-4703443 | [ 8 ] 3529118-4116280 | [ 13 ] 2941955-3529117 | [ 28 ] 2354792-2941954 |* [ 52 ] 1767629-2354791 |** [ 68 ] 1180466-1767628 |**** [ 141 ] 593303-1180465 |******* [ 246 ] 6141-593303 |************************************************** [ 1606 ] Storage Throughput = excellent ( 1656.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002786 bp ( 40002786 non ambiguous ) - Num Contigs Represented = 569 - 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.. : 167 raw families identified - RepeatScout: Running filtering stage.. 139 families remaining - RepeatScout: 00:03:26 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 125 families... 01:14:21 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 4 satellite(s), 52 contained, found in 00:00:07 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:07 (hh:mm:ss) Elapsed Time Round Time: 01:17:58 (hh:mm:ss) Elapsed Time : 69 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 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2945 repeats masked totaling 837827 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009286 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 10009286 bp After Masking: 8739067 bp Masked: 12.69 % -- Input Database Coverage: 10009286 bp out of 1168325350 bp ( 0.86 % ) Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:03:28 (hh:mm:ss) Elapsed Time, 3965 HSPs Collected Number of families returned by RECON: 324 Round Time: 00:03:56 (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 : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10438 repeats masked totaling 3229884 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033420 bp Num Contigs Represented = 479 Non ambiguous bp: Initial: 30033420 bp After Masking: 25389559 bp Masked: 15.46 % -- Input Database Coverage: 40042706 bp out of 1168325350 bp ( 3.43 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 298378 Comparison Time: 00:16:04 (hh:mm:ss) Elapsed Time, 11222 HSPs Collected Number of families returned by RECON: 1459 Round Time: 00:17:46 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32773 repeats masked totaling 9947485 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019197 bp Num Contigs Represented = 899 Non ambiguous bp: Initial: 90019197 bp After Masking: 75429631 bp Masked: 16.21 % -- Input Database Coverage: 130061903 bp out of 1168325350 bp ( 11.13 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2731953 Comparison Time: 01:38:03 (hh:mm:ss) Elapsed Time, 47977 HSPs Collected Number of families returned by RECON: 9806 Round Time: 01:42:56 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121510 repeats masked totaling 35774278 bp(s). - TE Masking time 00:03:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018710 bp Num Contigs Represented = 1350 Non ambiguous bp: Initial: 270018710 bp After Masking: 220435573 bp Masked: 18.36 % -- Input Database Coverage: 400080613 bp out of 1168325350 bp ( 34.24 % ) Sampling Time: 00:12:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24531510 Comparison Time: 11:58:33 (hh:mm:ss) Elapsed Time, 216331 HSPs Collected Number of families returned by RECON: 63552 Round Time: 12:34:29 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatScout/RECON discovery complete: 404 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.ArhgZB/RM_2259337.FriMar62226362026 # 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: 00:02:22 (hh:mm:ss) Elapsed Time Program Time: 15:59:27 (hh:mm:ss) Elapsed Time