RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KKHKyh/RM_2253136.ThuJun270645522024 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: 1719495951 Database = /dev/shm/rModeler.KKHKyh/GCF_036250125.1_bDixPip1.hap1 - Sequences = 696 - Bases = 1165201947 - N50 = 75926125 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145631753-156033950 | [ 1 ] 135229556-145631752 | [ ] 124827360-135229556 | [ ] 114425163-124827359 | [ 2 ] 104022966-114425162 | [ ] 93620770-104022966 | [ ] 83218573-93620769 | [ ] 72816376-83218572 | [ 3 ] 62414180-72816376 | [ 2 ] 52011983-62414179 | [ ] 41609786-52011982 | [ ] 31207590-41609786 | [ 3 ] 20805393-31207589 | [ 5 ] 10403196-20805392 | [ 7 ] 1000-10403196 |************************************************** [ 673 ] Storage Throughput = excellent ( 1183.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035604 bp ( 40032404 non ambiguous ) - Num Contigs Represented = 71 - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:24 (hh:mm:ss) Elapsed Time Round Time: 00:22:49 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2950 repeats masked totaling 896658 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040147 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10039347 bp After Masking: 8858136 bp Masked: 11.77 % -- Input Database Coverage: 10040147 bp out of 1165201947 bp ( 0.86 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:34 (hh:mm:ss) Elapsed Time, 644 HSPs Collected Number of families returned by RECON: 262 Round Time: 00:07:59 (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 : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8658 repeats masked totaling 2695450 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035388 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30032988 bp After Masking: 26346230 bp Masked: 12.28 % -- Input Database Coverage: 40075535 bp out of 1165201947 bp ( 3.44 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:32:11 (hh:mm:ss) Elapsed Time, 10453 HSPs Collected Number of families returned by RECON: 1478 Round Time: 00:37:07 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28380 repeats masked totaling 8481672 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022914 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 90018737 bp After Masking: 79079297 bp Masked: 12.15 % -- Input Database Coverage: 130098449 bp out of 1165201947 bp ( 11.17 % ) Sampling Time: 00:10:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:36:33 (hh:mm:ss) Elapsed Time, 66504 HSPs Collected Number of families returned by RECON: 9093 Round Time: 04:07:55 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97205 repeats masked totaling 31529338 bp(s). - TE Masking time 00:05:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031268 bp Num Contigs Represented = 285 Non ambiguous bp: Initial: 270016095 bp After Masking: 231845840 bp Masked: 14.14 % -- Input Database Coverage: 400129717 bp out of 1165201947 bp ( 34.34 % ) Sampling Time: 00:32:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 29:22:11 (hh:mm:ss) Elapsed Time, 271261 HSPs Collected Number of families returned by RECON: 61231 Round Time: 30:27:22 (hh:mm:ss) Elapsed Time : 272 families discovered. RepeatScout/RECON discovery complete: 519 families found Classification Time: 00:39:13 (hh:mm:ss) Elapsed Time Program Time: 36:22:25 (hh:mm:ss) Elapsed Time