RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.lPZ4P7/RM_1164709.TueNov121201592024 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: 1731441719 Database = /scratch/tmp/rModeler.lPZ4P7/GCA_036971685.1_bPatFas1.hap2 - Sequences = 453 - Bases = 1410058165 - N50 = 80804424 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201223936-215596151 | [ 1 ] 186851721-201223935 | [ ] 172479507-186851721 | [ ] 158107292-172479506 | [ 1 ] 143735077-158107291 | [ ] 129362863-143735077 | [ ] 114990648-129362862 | [ 1 ] 100618433-114990647 | [ ] 86246219-100618433 | [ ] 71874004-86246218 | [ 2 ] 57501789-71874003 | [ 1 ] 43129575-57501789 | [ 2 ] 28757360-43129574 | [ 2 ] 14385145-28757359 |* [ 10 ] 12931-14385145 |************************************************** [ 433 ] Storage Throughput = excellent ( 1649.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40416317 bp ( 40010280 non ambiguous ) - Num Contigs Represented = 122 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:07 (hh:mm:ss) Elapsed Time Round Time: 00:12:20 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2521 repeats masked totaling 1051616 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10095763 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10015763 bp After Masking: 7894651 bp Masked: 21.18 % -- Input Database Coverage: 10095763 bp out of 1410058165 bp ( 0.72 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 13040 HSPs Collected Number of families returned by RECON: 182 Round Time: 00:05:12 (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 : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9017 repeats masked totaling 3557949 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30360476 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 30034439 bp After Masking: 23916545 bp Masked: 20.37 % -- Input Database Coverage: 40456239 bp out of 1410058165 bp ( 2.87 % ) Sampling Time: 00:08:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:14:16 (hh:mm:ss) Elapsed Time, 130743 HSPs Collected Number of families returned by RECON: 1068 Round Time: 00:23:00 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26634 repeats masked totaling 9548693 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90477883 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 90016107 bp After Masking: 72822534 bp Masked: 19.10 % -- Input Database Coverage: 130934122 bp out of 1410058165 bp ( 9.29 % ) Sampling Time: 00:24:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:32:54 (hh:mm:ss) Elapsed Time, 1497841 HSPs Collected Number of families returned by RECON: 6110 Round Time: 01:58:50 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90605 repeats masked totaling 32646832 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271504506 bp Num Contigs Represented = 299 Non ambiguous bp: Initial: 270005877 bp After Masking: 216039481 bp Masked: 19.99 % -- Input Database Coverage: 402438628 bp out of 1410058165 bp ( 28.54 % ) Sampling Time: 01:09:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 11:22:53 (hh:mm:ss) Elapsed Time, 13236448 HSPs Collected Number of families returned by RECON: 38613 Round Time: 12:45:03 (hh:mm:ss) Elapsed Time : 257 families discovered. RepeatScout/RECON discovery complete: 477 families found Classification Time: 00:21:28 (hh:mm:ss) Elapsed Time Program Time: 15:45:53 (hh:mm:ss) Elapsed Time