RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.RDnyAz/RM_1024095.TueNov190857582024 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: 1732035478 Database = /data/tmp/rModeler.RDnyAz/GCF_902635505.1_mSarHar1.11 - Sequences = 106 - Bases = 3086674442 - N50 = 662751787 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 668652899-716413629 | [ 1 ] 620892169-668652899 | [ 1 ] 573131439-620892169 | [ 1 ] 525370709-573131439 | [ ] 477609979-525370709 | [ ] 429849249-477609979 | [ 1 ] 382088519-429849249 | [ ] 334327789-382088519 | [ ] 286567059-334327789 | [ 1 ] 238806329-286567059 | [ 1 ] 191045599-238806329 | [ ] 143284869-191045599 | [ ] 95524139-143284869 | [ ] 47763409-95524139 | [ 1 ] 2679-47763409 |************************************************** [ 99 ] Storage Throughput = excellent ( 1299.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003592 bp ( 40003192 non ambiguous ) - Num Contigs Represented = 10 - Sequence extraction : 00:11:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:12 (hh:mm:ss) Elapsed Time Round Time: 00:37:16 (hh:mm:ss) Elapsed Time : 294 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15908 repeats masked totaling 3193759 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039986 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 10039786 bp After Masking: 6719817 bp Masked: 33.07 % -- Input Database Coverage: 10039986 bp out of 3086674442 bp ( 0.33 % ) Sampling Time: 00:03:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:16 (hh:mm:ss) Elapsed Time, 14392 HSPs Collected Number of families returned by RECON: 1557 Round Time: 00:12:03 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56791 repeats masked totaling 11688141 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003606 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 30003406 bp After Masking: 17946862 bp Masked: 40.18 % -- Input Database Coverage: 40043592 bp out of 3086674442 bp ( 1.30 % ) Sampling Time: 00:09:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:28:31 (hh:mm:ss) Elapsed Time, 26704 HSPs Collected Number of families returned by RECON: 3005 Round Time: 00:41:53 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:22:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 183727 repeats masked totaling 38246777 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029324 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 90027764 bp After Masking: 50662318 bp Masked: 43.73 % -- Input Database Coverage: 130072916 bp out of 3086674442 bp ( 4.21 % ) Sampling Time: 00:28:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:46:39 (hh:mm:ss) Elapsed Time, 82756 HSPs Collected Number of families returned by RECON: 10032 Round Time: 03:29:02 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:09:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 599505 repeats masked totaling 122593187 bp(s). - TE Masking time 00:06:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027851 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 270024151 bp After Masking: 144156839 bp Masked: 46.61 % -- Input Database Coverage: 400100767 bp out of 3086674442 bp ( 12.96 % ) Sampling Time: 01:31:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 25:51:27 (hh:mm:ss) Elapsed Time, 214176 HSPs Collected Number of families returned by RECON: 39114 Round Time: 28:37:08 (hh:mm:ss) Elapsed Time : 470 families discovered. RepeatScout/RECON discovery complete: 1052 families found Classification Time: 00:32:11 (hh:mm:ss) Elapsed Time Program Time: 34:09:33 (hh:mm:ss) Elapsed Time