RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.JoJKh2/RM_2132512.ThuSep110023152025 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: 1757575394 Database = /dev/shm/rModeler.JoJKh2/GCA_021018975.2_ASM2101897v2 - Sequences = 1808 - Bases = 14408920 - N50 = 28682 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188462-201910 | [ 1 ] 175015-188462 | [ ] 161568-175015 | [ 3 ] 148120-161567 | [ ] 134673-148120 | [ 1 ] 121226-134673 | [ 1 ] 107778-121225 | [ ] 94331-107778 | [ 4 ] 80884-94331 | [ 6 ] 67436-80883 | [ 4 ] 53989-67436 | [ 13 ] 40542-53989 |* [ 39 ] 27094-40541 |** [ 85 ] 13647-27094 |***** [ 165 ] 200-13647 |************************************************** [ 1486 ] Storage Throughput = excellent ( 1538.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14408824 bp ( 14067082 non ambiguous ) - Num Contigs Represented = 1808 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 30 raw families identified - RepeatScout: Running filtering stage.. 30 families remaining - RepeatScout: 00:00:58 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 28 families... 00:00:11 (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: 00:01:12 (hh:mm:ss) Elapsed Time : 25 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 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 491 repeats masked totaling 138923 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10255086 bp Num Contigs Represented = 1283 Non ambiguous bp: Initial: 10010468 bp After Masking: 9837394 bp Masked: 1.73 % -- Input Database Coverage: 10255086 bp out of 14408920 bp ( 71.17 % ) Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 901153 Comparison Time: 00:08:58 (hh:mm:ss) Elapsed Time, 5550 HSPs Collected Number of families returned by RECON: 1284 Round Time: 00:09:22 (hh:mm:ss) Elapsed Time : 3 families discovered. - Increasing sample size to include end piece now = 34408920 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34408920 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... 210 repeats masked totaling 55227 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4153683 bp Num Contigs Represented = 561 Non ambiguous bp: Initial: 4056559 bp After Masking: 3986315 bp Masked: 1.73 % -- Input Database Coverage: 14408769 bp out of 14408920 bp ( 100.00 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 161596 Comparison Time: 00:03:08 (hh:mm:ss) Elapsed Time, 712 HSPs Collected Number of families returned by RECON: 316 Round Time: 00:03:15 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 28 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.JoJKh2/RM_2132512.ThuSep110023152025 # 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: 00:00:07 (hh:mm:ss) Elapsed Time Program Time: 00:13:56 (hh:mm:ss) Elapsed Time