RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8CAR0v/RM_47467.WedDec282102432022 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1672290162 Database = /dev/shm/rModeler.8CAR0v/GCF_900634625.1_fParRan2.1 - Sequences = 156 - Bases = 551012959 - N50 = 23963493 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 43590407-46703924 | [ 1 ] 40476890-43590406 | [ ] 37363373-40476889 | [ ] 34249856-37363372 | [ ] 31136340-34249856 | [ 1 ] 28022823-31136339 | [ ] 24909306-28022822 |* [ 3 ] 21795789-24909305 |*** [ 10 ] 18682272-21795788 |* [ 3 ] 15568756-18682272 |* [ 3 ] 12455239-15568755 | [ 1 ] 9341722-12455238 | [ 1 ] 6228205-9341721 | [ ] 3114688-6228204 | [ 2 ] 1172-3114688 |************************************************** [ 131 ] Storage Throughput = excellent ( 1144.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40667341 bp ( 40018153 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:33 (hh:mm:ss) Elapsed Time Round Time: 00:18:40 (hh:mm:ss) Elapsed Time : 395 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5194 repeats masked totaling 1217266 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10202081 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10033802 bp After Masking: 8619943 bp Masked: 14.09 % -- Input Database Coverage: 10202081 bp out of 551012959 bp ( 1.85 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:07 (hh:mm:ss) Elapsed Time, 4238 HSPs Collected Number of families returned by RECON: 1136 Round Time: 00:07:16 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17212 repeats masked totaling 4146311 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30505172 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30024263 bp After Masking: 25302492 bp Masked: 15.73 % -- Input Database Coverage: 40707253 bp out of 551012959 bp ( 7.39 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:30:00 (hh:mm:ss) Elapsed Time, 32418 HSPs Collected Number of families returned by RECON: 4781 Round Time: 00:33:12 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54011 repeats masked totaling 11788267 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91540618 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90012925 bp After Masking: 76654679 bp Masked: 14.84 % -- Input Database Coverage: 132247871 bp out of 551012959 bp ( 24.00 % ) Sampling Time: 00:07:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2657665 Comparison Time: 03:35:11 (hh:mm:ss) Elapsed Time, 192555 HSPs Collected Number of families returned by RECON: 20942 Round Time: 03:57:32 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 200708 repeats masked totaling 44626165 bp(s). - TE Masking time 00:09:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275253647 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 270014563 bp After Masking: 220855599 bp Masked: 18.21 % -- Input Database Coverage: 407501518 bp out of 551012959 bp ( 73.95 % ) Sampling Time: 00:30:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23891328 Comparison Time: 29:17:47 (hh:mm:ss) Elapsed Time, 904868 HSPs Collected Number of families returned by RECON: 90045 Round Time: 31:58:09 (hh:mm:ss) Elapsed Time : 804 families discovered. RepeatScout/RECON discovery complete: 1543 families found Classification Time: 01:55:10 (hh:mm:ss) Elapsed Time Program Time: 38:49:59 (hh:mm:ss) Elapsed Time