RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ubkHJO/RM_2461351.WedDec41605572024 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: 1733357157 Database = /scratch/tmp/rModeler.ubkHJO/GCA_964237395.1_bGalChl1.hap2.1 - Sequences = 395 - Bases = 1208559276 - N50 = 123325843 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 199444124-213690062 | [ 1 ] 185198187-199444124 | [ ] 170952249-185198186 | [ ] 156706312-170952249 | [ 1 ] 142460374-156706311 | [ ] 128214437-142460374 | [ ] 113968499-128214436 | [ 1 ] 99722562-113968499 | [ ] 85476624-99722561 | [ 2 ] 71230687-85476624 | [ 1 ] 56984749-71230686 | [ ] 42738812-56984749 | [ ] 28492874-42738811 | [ 3 ] 14246937-28492874 |* [ 10 ] 1000-14246937 |************************************************** [ 376 ] Storage Throughput = excellent ( 1422.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005068 bp ( 40001268 non ambiguous ) - Num Contigs Represented = 74 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:19 (hh:mm:ss) Elapsed Time Round Time: 00:10:51 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3079 repeats masked totaling 865949 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033253 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10032053 bp After Masking: 8785580 bp Masked: 12.42 % -- Input Database Coverage: 10033253 bp out of 1208559276 bp ( 0.83 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 340 HSPs Collected Number of families returned by RECON: 184 Round Time: 00:03:22 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10111 repeats masked totaling 2866968 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011892 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30009292 bp After Masking: 26226640 bp Masked: 12.60 % -- Input Database Coverage: 40045145 bp out of 1208559276 bp ( 3.31 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:02 (hh:mm:ss) Elapsed Time, 10235 HSPs Collected Number of families returned by RECON: 1327 Round Time: 00:15:01 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30779 repeats masked totaling 8456863 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011924 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 90003359 bp After Masking: 78558097 bp Masked: 12.72 % -- Input Database Coverage: 130057069 bp out of 1208559276 bp ( 10.76 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:22:30 (hh:mm:ss) Elapsed Time, 42807 HSPs Collected Number of families returned by RECON: 8675 Round Time: 01:30:00 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107884 repeats masked totaling 29910588 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035511 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 270011076 bp After Masking: 232823795 bp Masked: 13.77 % -- Input Database Coverage: 400092580 bp out of 1208559276 bp ( 33.10 % ) Sampling Time: 00:15:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 10:26:39 (hh:mm:ss) Elapsed Time, 231835 HSPs Collected Number of families returned by RECON: 58317 Round Time: 11:09:48 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatScout/RECON discovery complete: 442 families found Classification Time: 00:29:02 (hh:mm:ss) Elapsed Time Program Time: 13:38:04 (hh:mm:ss) Elapsed Time