RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.WrgX4Y/RM_1994164.TueAug180339572026 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: 1787049596 Database = /dev/shm/rModeler.WrgX4Y/GCF_929443795.2_bAccGen1.2 - Sequences = 454 - Bases = 1398011397 - N50 = 37312042 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 83780511-89764762 | [ 1 ] 77796260-83780510 | [ ] 71812009-77796259 | [ ] 65827758-71812008 | [ ] 59843508-65827758 | [ ] 53859257-59843507 | [ 2 ] 47875006-53859256 | [ 2 ] 41890755-47875005 | [ 5 ] 35906504-41890754 | [ 4 ] 29922254-35906504 | [ 5 ] 23938003-29922253 | [ 7 ] 17953752-23938002 |* [ 9 ] 11969501-17953751 | [ 1 ] 5985250-11969500 | [ 2 ] 1000-5985250 |************************************************** [ 416 ] Storage Throughput = excellent ( 1666.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029157 bp ( 40028157 non ambiguous ) - Num Contigs Represented = 105 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 104 raw families identified - RepeatScout: Running filtering stage.. 96 families remaining - RepeatScout: 00:03:11 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 92 families... 00:18:44 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 38 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time Round Time: 00:22:15 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1748 repeats masked totaling 946044 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013144 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10013144 bp After Masking: 8581036 bp Masked: 14.30 % -- Input Database Coverage: 10013144 bp out of 1398011397 bp ( 0.72 % ) Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 12478 HSPs Collected Number of families returned by RECON: 336 Round Time: 00:06:20 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4536 repeats masked totaling 2158182 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016011 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 30015011 bp After Masking: 25120754 bp Masked: 16.31 % -- Input Database Coverage: 40029155 bp out of 1398011397 bp ( 2.86 % ) Sampling Time: 00:02:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:25:24 (hh:mm:ss) Elapsed Time, 40577 HSPs Collected Number of families returned by RECON: 1260 Round Time: 00:30:40 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17296 repeats masked totaling 7659584 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005314 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 90002914 bp After Masking: 75492932 bp Masked: 16.12 % -- Input Database Coverage: 130034469 bp out of 1398011397 bp ( 9.30 % ) Sampling Time: 00:05:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 02:19:17 (hh:mm:ss) Elapsed Time, 412247 HSPs Collected Number of families returned by RECON: 7901 Round Time: 02:26:50 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75629 repeats masked totaling 27579065 bp(s). - TE Masking time 00:03:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035281 bp Num Contigs Represented = 235 Non ambiguous bp: Initial: 270027481 bp After Masking: 221040265 bp Masked: 18.14 % -- Input Database Coverage: 400069750 bp out of 1398011397 bp ( 28.62 % ) Sampling Time: 00:15:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 13:39:54 (hh:mm:ss) Elapsed Time, 14004658 HSPs Collected Number of families returned by RECON: 46340 Round Time: 14:11:56 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatScout/RECON discovery complete: 338 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.WrgX4Y/RM_1994164.TueAug180339572026 # 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: 00:02:14 (hh:mm:ss) Elapsed Time Program Time: 17:40:15 (hh:mm:ss) Elapsed Time