RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9PzDmZ/RM_2821145.SunJul201857382025 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: 1753063057 Database = /dev/shm/rModeler.9PzDmZ/GCA_965203405.1_mPipPip2.hap1.1 - Sequences = 575 - Bases = 1899371011 - N50 = 99565056 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195264619-209212021 | [ 1 ] 181317218-195264619 | [ 2 ] 167369816-181317217 | [ ] 153422415-167369816 | [ ] 139475014-153422415 | [ ] 125527612-139475013 | [ ] 111580211-125527612 | [ ] 97632809-111580210 | [ 3 ] 83685408-97632809 | [ 3 ] 69738007-83685408 | [ 3 ] 55790605-69738006 | [ 2 ] 41843204-55790605 | [ 5 ] 27895802-41843203 | [ ] 13948401-27895802 | [ 3 ] 1000-13948401 |************************************************** [ 553 ] Storage Throughput = excellent ( 1940.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028833 bp ( 40022633 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:02 (hh:mm:ss) Elapsed Time Round Time: 00:10:47 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (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... 14516 repeats masked totaling 2414771 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037170 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10035970 bp After Masking: 7213747 bp Masked: 28.12 % -- Input Database Coverage: 10037170 bp out of 1899371011 bp ( 0.53 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 16808 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:03:37 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46045 repeats masked totaling 7577033 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031505 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30026505 bp After Masking: 20902989 bp Masked: 30.38 % -- Input Database Coverage: 40068675 bp out of 1899371011 bp ( 2.11 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:12:37 (hh:mm:ss) Elapsed Time, 83392 HSPs Collected Number of families returned by RECON: 2392 Round Time: 00:14:46 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143297 repeats masked totaling 23726242 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048933 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90033933 bp After Masking: 61334854 bp Masked: 31.88 % -- Input Database Coverage: 130117608 bp out of 1899371011 bp ( 6.85 % ) Sampling Time: 00:05:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:19:25 (hh:mm:ss) Elapsed Time, 2669579 HSPs Collected Number of families returned by RECON: 8501 Round Time: 01:26:52 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 475135 repeats masked totaling 79239581 bp(s). - TE Masking time 00:02:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063227 bp Num Contigs Represented = 169 Non ambiguous bp: Initial: 270013158 bp After Masking: 176369777 bp Masked: 34.68 % -- Input Database Coverage: 400180835 bp out of 1899371011 bp ( 21.07 % ) Sampling Time: 00:17:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23021505 Comparison Time: 09:24:24 (hh:mm:ss) Elapsed Time, 19076297 HSPs Collected Number of families returned by RECON: 34929 Round Time: 09:54:08 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatScout/RECON discovery complete: 1022 families found Classification Time: 00:17:35 (hh:mm:ss) Elapsed Time Program Time: 12:07:45 (hh:mm:ss) Elapsed Time