RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.3Bld8w/RM_3265792.MonSep81903472025 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: 1757383427 Database = /dev/shm/rModeler.3Bld8w/GCA_002864135.1_ASM286413v1 - Sequences = 3872 - Bases = 42468207 - N50 = 139057 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 581393-622907 | [ 1 ] 539879-581392 | [ ] 498365-539878 | [ ] 456851-498364 | [ 2 ] 415338-456851 | [ 2 ] 373824-415337 | [ 5 ] 332310-373823 | [ 4 ] 290796-332309 | [ 7 ] 249282-290795 | [ 6 ] 207769-249282 | [ 18 ] 166255-207768 | [ 22 ] 124741-166254 | [ 36 ] 83227-124740 |* [ 72 ] 41713-83226 |* [ 105 ] 200-41713 |************************************************** [ 3592 ] Storage Throughput = excellent ( 1649.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023553 bp ( 40009720 non ambiguous ) - Num Contigs Represented = 3593 - 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.. : 90 raw families identified - RepeatScout: Running filtering stage.. 43 families remaining - RepeatScout: 00:00:45 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 39 families... 00:00:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:58 (hh:mm:ss) Elapsed Time : 36 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... 517 repeats masked totaling 131218 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005736 bp Num Contigs Represented = 943 Non ambiguous bp: Initial: 10001749 bp After Masking: 9861937 bp Masked: 1.40 % -- Input Database Coverage: 10005736 bp out of 42468207 bp ( 23.56 % ) Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 527878 Comparison Time: 00:06:25 (hh:mm:ss) Elapsed Time, 13691 HSPs Collected Number of families returned by RECON: 878 Round Time: 00:07:41 (hh:mm:ss) Elapsed Time : 10 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 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3229 repeats masked totaling 713668 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017737 bp Num Contigs Represented = 2809 Non ambiguous bp: Initial: 30007891 bp After Masking: 29267350 bp Masked: 2.47 % -- Input Database Coverage: 40023473 bp out of 42468207 bp ( 94.24 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5430160 Comparison Time: 00:24:42 (hh:mm:ss) Elapsed Time, 24094 HSPs Collected Number of families returned by RECON: 3645 Round Time: 00:27:46 (hh:mm:ss) Elapsed Time : 20 families discovered. - Increasing sample size to include end piece now = 92462471 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 92462471 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 359 repeats masked totaling 89118 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2444549 bp Num Contigs Represented = 330 Non ambiguous bp: Initial: 2444035 bp After Masking: 2353741 bp Masked: 3.69 % -- Input Database Coverage: 42468022 bp out of 42468207 bp ( 100.00 % ) Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 56616 Comparison Time: 00:01:38 (hh:mm:ss) Elapsed Time, 103 HSPs Collected Number of families returned by RECON: 53 Round Time: 00:01:50 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 66 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.3Bld8w/RM_3265792.MonSep81903472025 # 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: 00:00:16 (hh:mm:ss) Elapsed Time Program Time: 00:38:31 (hh:mm:ss) Elapsed Time