RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aZZzJ4/RM_383706.MonJan21000572023 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: 1672682456 Database = /dev/shm/rModeler.aZZzJ4/GCF_009762535.1_fNotCel1.pri - Sequences = 467 - Bases = 846744125 - N50 = 37353604 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39550900-42375795 | [ 5 ] 36726005-39550899 | [ 6 ] 33901111-36726005 | [ 4 ] 31076216-33901110 | [ 4 ] 28251321-31076215 | [ 3 ] 25426427-28251321 | [ 1 ] 22601532-25426426 | [ ] 19776637-22601531 | [ ] 16951743-19776637 | [ ] 14126848-16951742 | [ ] 11301953-14126847 | [ 1 ] 8477059-11301953 | [ ] 5652164-8477058 | [ ] 2827269-5652163 | [ ] 2375-2827269 |************************************************** [ 443 ] Storage Throughput = excellent ( 1551.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40574712 bp ( 40014016 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:54 (hh:mm:ss) Elapsed Time Round Time: 00:16:25 (hh:mm:ss) Elapsed Time : 553 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10274 repeats masked totaling 2235109 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10130917 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10001132 bp After Masking: 7262658 bp Masked: 27.38 % -- Input Database Coverage: 10130917 bp out of 846744125 bp ( 1.20 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 6957 HSPs Collected Number of families returned by RECON: 1086 Round Time: 00:06:23 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33585 repeats masked totaling 7111014 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30443789 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30012878 bp After Masking: 21612065 bp Masked: 27.99 % -- Input Database Coverage: 40574706 bp out of 846744125 bp ( 4.79 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:21:40 (hh:mm:ss) Elapsed Time, 40559 HSPs Collected Number of families returned by RECON: 4111 Round Time: 00:25:07 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108989 repeats masked totaling 23008939 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91506741 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 90035828 bp After Masking: 62986078 bp Masked: 30.04 % -- Input Database Coverage: 132081447 bp out of 846744125 bp ( 15.60 % ) Sampling Time: 00:08:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2687721 Comparison Time: 02:05:16 (hh:mm:ss) Elapsed Time, 223385 HSPs Collected Number of families returned by RECON: 14837 Round Time: 02:20:08 (hh:mm:ss) Elapsed Time : 498 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 395236 repeats masked totaling 81517317 bp(s). - TE Masking time 00:06:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275065246 bp Num Contigs Represented = 231 Non ambiguous bp: Initial: 270001961 bp After Masking: 176316799 bp Masked: 34.70 % -- Input Database Coverage: 407146693 bp out of 846744125 bp ( 48.08 % ) Sampling Time: 00:30:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24231241 Comparison Time: 13:35:44 (hh:mm:ss) Elapsed Time, 532027 HSPs Collected Number of families returned by RECON: 53830 Round Time: 14:53:30 (hh:mm:ss) Elapsed Time : 991 families discovered. RepeatScout/RECON discovery complete: 2140 families found Classification Time: 00:52:57 (hh:mm:ss) Elapsed Time Program Time: 18:54:30 (hh:mm:ss) Elapsed Time