RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ekgOpw/RM_2347123.ThuNov140034312024 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: 1731573271 Database = /scratch/tmp/rModeler.ekgOpw/GCA_964237585.1_bGalChl1.hap1.1 - Sequences = 818 - Bases = 1282411533 - N50 = 92355778 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201496241-215888759 | [ 1 ] 187103724-201496241 | [ ] 172711207-187103724 | [ ] 158318689-172711206 | [ 1 ] 143926172-158318689 | [ ] 129533655-143926172 | [ ] 115141138-129533655 | [ 1 ] 100748620-115141137 | [ ] 86356103-100748620 | [ 2 ] 71963586-86356103 | [ 1 ] 57571069-71963586 | [ ] 43178551-57571068 | [ ] 28786034-43178551 | [ 3 ] 14393517-28786034 | [ 10 ] 1000-14393517 |************************************************** [ 799 ] Storage Throughput = excellent ( 1571.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034054 bp ( 40031654 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:08 (hh:mm:ss) Elapsed Time Round Time: 00:10:10 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3772 repeats masked totaling 978512 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001187 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10000387 bp After Masking: 8193493 bp Masked: 18.07 % -- Input Database Coverage: 10001187 bp out of 1282411533 bp ( 0.78 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 867 HSPs Collected Number of families returned by RECON: 244 Round Time: 00:03:42 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11097 repeats masked totaling 2917014 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032866 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30031266 bp After Masking: 25417980 bp Masked: 15.36 % -- Input Database Coverage: 40034053 bp out of 1282411533 bp ( 3.12 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:12:40 (hh:mm:ss) Elapsed Time, 3785 HSPs Collected Number of families returned by RECON: 1285 Round Time: 00:15:00 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31815 repeats masked totaling 8056693 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035374 bp Num Contigs Represented = 199 Non ambiguous bp: Initial: 90024609 bp After Masking: 75452651 bp Masked: 16.19 % -- Input Database Coverage: 130069427 bp out of 1282411533 bp ( 10.14 % ) Sampling Time: 00:06:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 01:20:41 (hh:mm:ss) Elapsed Time, 44834 HSPs Collected Number of families returned by RECON: 8287 Round Time: 01:34:04 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112480 repeats masked totaling 29147392 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064059 bp Num Contigs Represented = 366 Non ambiguous bp: Initial: 270038375 bp After Masking: 221702476 bp Masked: 17.90 % -- Input Database Coverage: 400133486 bp out of 1282411533 bp ( 31.20 % ) Sampling Time: 00:23:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 11:26:16 (hh:mm:ss) Elapsed Time, 259940 HSPs Collected Number of families returned by RECON: 53479 Round Time: 12:05:14 (hh:mm:ss) Elapsed Time : 264 families discovered. RepeatScout/RECON discovery complete: 463 families found Classification Time: 00:26:45 (hh:mm:ss) Elapsed Time Program Time: 14:34:55 (hh:mm:ss) Elapsed Time