RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Jxmkpy/RM_3525691.ThuSep41258562025 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: 1757015936 Database = /dev/shm/rModeler.Jxmkpy/GCA_045362485.1_fLetNeb1.hap2 - Sequences = 151 - Bases = 1122130221 - N50 = 49183514 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 51886951-55592287 |* [ 3 ] 48181615-51886951 |** [ 7 ] 44476279-48181615 |** [ 6 ] 40770943-44476279 |* [ 4 ] 37065607-40770943 | [ 2 ] 33360271-37065607 | [ 1 ] 29654935-33360271 | [ 1 ] 25949599-29654935 | [ ] 22244263-25949599 | [ ] 18538927-22244263 | [ ] 14833591-18538927 | [ ] 11128255-14833591 | [ ] 7422919-11128255 | [ ] 3717583-7422919 | [ ] 12247-3717583 |************************************************** [ 127 ] Storage Throughput = excellent ( 1668.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015584 bp ( 40012384 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 604 raw families identified - RepeatScout: Running filtering stage.. 565 families remaining - RepeatScout: 00:01:52 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 535 families... 00:30:34 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 7 satellite(s), 188 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:32:51 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8854 repeats masked totaling 1549708 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031148 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10029748 bp After Masking: 8184532 bp Masked: 18.40 % -- Input Database Coverage: 10031148 bp out of 1122130221 bp ( 0.89 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:01 (hh:mm:ss) Elapsed Time, 37652 HSPs Collected Number of families returned by RECON: 2739 Round Time: 00:05:08 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40059 repeats masked totaling 7013537 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024436 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30022636 bp After Masking: 22060388 bp Masked: 26.52 % -- Input Database Coverage: 40055584 bp out of 1122130221 bp ( 3.57 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:16:57 (hh:mm:ss) Elapsed Time, 131244 HSPs Collected Number of families returned by RECON: 7057 Round Time: 00:20:16 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155294 repeats masked totaling 26480733 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025307 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90021407 bp After Masking: 60504060 bp Masked: 32.79 % -- Input Database Coverage: 130080891 bp out of 1122130221 bp ( 11.59 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:34:11 (hh:mm:ss) Elapsed Time, 446368 HSPs Collected Number of families returned by RECON: 17163 Round Time: 01:45:55 (hh:mm:ss) Elapsed Time : 576 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 601706 repeats masked totaling 100730586 bp(s). - TE Masking time 00:07:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034682 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 270023382 bp After Masking: 161573513 bp Masked: 40.16 % -- Input Database Coverage: 400115573 bp out of 1122130221 bp ( 35.66 % ) Sampling Time: 00:18:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 10:22:35 (hh:mm:ss) Elapsed Time, 1288272 HSPs Collected Number of families returned by RECON: 47431 Round Time: 11:11:53 (hh:mm:ss) Elapsed Time : 1433 families discovered. RepeatScout/RECON discovery complete: 2614 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Jxmkpy/RM_3525691.ThuSep41258562025 # 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: 00:04:17 (hh:mm:ss) Elapsed Time Program Time: 14:00:20 (hh:mm:ss) Elapsed Time