RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZiSK2m/RM_47216.FriDec301411462022 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: 1672438306 Database = /dev/shm/rModeler.ZiSK2m/GCF_900634415.1_fCotGob3.1 - Sequences = 322 - Bases = 609391784 - N50 = 25704503 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 28447705-30479438 | [ 4 ] 26415973-28447705 | [ 5 ] 24384240-26415972 | [ 3 ] 22352508-24384240 |* [ 6 ] 20320775-22352507 | [ 2 ] 18289043-20320775 | [ ] 16257310-18289042 | [ 1 ] 14225578-16257310 | [ 2 ] 12193845-14225577 | [ 1 ] 10162113-12193845 | [ ] 8130380-10162112 | [ ] 6098648-8130380 | [ ] 4066915-6098647 | [ ] 2035183-4066915 | [ ] 3451-2035183 |************************************************** [ 298 ] Storage Throughput = excellent ( 1154.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40117925 bp ( 40034807 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:54 (hh:mm:ss) Elapsed Time Round Time: 00:20:48 (hh:mm:ss) Elapsed Time : 433 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 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6798 repeats masked totaling 1110690 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033172 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10032596 bp After Masking: 8300037 bp Masked: 17.27 % -- Input Database Coverage: 10033172 bp out of 609391784 bp ( 1.65 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:33 (hh:mm:ss) Elapsed Time, 6392 HSPs Collected Number of families returned by RECON: 1374 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 16 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 00:06:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21570 repeats masked totaling 3326542 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30084673 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30002131 bp After Masking: 24656480 bp Masked: 17.82 % -- Input Database Coverage: 40117845 bp out of 609391784 bp ( 6.58 % ) Sampling Time: 00:07:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:29:12 (hh:mm:ss) Elapsed Time, 45669 HSPs Collected Number of families returned by RECON: 5318 Round Time: 00:38:49 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75617 repeats masked totaling 12256194 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90270646 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 90034863 bp After Masking: 72129173 bp Masked: 19.89 % -- Input Database Coverage: 130388491 bp out of 609391784 bp ( 21.40 % ) Sampling Time: 00:24:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:34:53 (hh:mm:ss) Elapsed Time, 238577 HSPs Collected Number of families returned by RECON: 18864 Round Time: 04:09:58 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 288067 repeats masked totaling 47313167 bp(s). - TE Masking time 00:06:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271150972 bp Num Contigs Represented = 238 Non ambiguous bp: Initial: 270031997 bp After Masking: 205878470 bp Masked: 23.76 % -- Input Database Coverage: 401539463 bp out of 609391784 bp ( 65.89 % ) Sampling Time: 01:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23403061 Comparison Time: 25:48:35 (hh:mm:ss) Elapsed Time, 735777 HSPs Collected Number of families returned by RECON: 71157 Round Time: 28:22:09 (hh:mm:ss) Elapsed Time : 1121 families discovered. RepeatScout/RECON discovery complete: 2094 families found Classification Time: 01:16:08 (hh:mm:ss) Elapsed Time Program Time: 34:55:56 (hh:mm:ss) Elapsed Time