RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.swYN2w/RM_1223703.FriSep120927002025 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: 1757694419 Database = /dev/shm/rModeler.swYN2w/GCA_040822265.1_ASM4082226v1 - Sequences = 12 - Bases = 45827615 Storage Throughput = excellent ( 1478.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030683 bp ( 40030683 non ambiguous ) - Num Contigs Represented = 11 - 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.. : 55 raw families identified - RepeatScout: Running filtering stage.. 48 families remaining - RepeatScout: 00:00:59 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 47 families... 00:36:13 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 2 satellite(s), 12 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:37:19 (hh:mm:ss) Elapsed Time : 34 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... 761 repeats masked totaling 484610 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011606 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 10011606 bp After Masking: 9516335 bp Masked: 4.95 % -- Input Database Coverage: 10011606 bp out of 45827615 bp ( 21.85 % ) Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:39 (hh:mm:ss) Elapsed Time, 2787 HSPs Collected Number of families returned by RECON: 589 Round Time: 00:05:58 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (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... 2221 repeats masked totaling 1535791 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018997 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 30018997 bp After Masking: 28448509 bp Masked: 5.23 % -- Input Database Coverage: 40030603 bp out of 45827615 bp ( 87.35 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:15:06 (hh:mm:ss) Elapsed Time, 28788 HSPs Collected Number of families returned by RECON: 3151 Round Time: 00:22:19 (hh:mm:ss) Elapsed Time : 12 families discovered. - Increasing sample size to include end piece now = 95816009 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 95816009 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 455 repeats masked totaling 263892 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 5796879 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 5796879 bp After Masking: 5529183 bp Masked: 4.62 % -- Input Database Coverage: 45827482 bp out of 45827615 bp ( 100.00 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 10731 Comparison Time: 00:01:53 (hh:mm:ss) Elapsed Time, 324 HSPs Collected Number of families returned by RECON: 218 Round Time: 00:02:36 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 48 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.swYN2w/RM_1223703.FriSep120927002025 # 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: 00:00:18 (hh:mm:ss) Elapsed Time Program Time: 01:08:30 (hh:mm:ss) Elapsed Time