RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4fdqsM/RM_9156.TueDec52113112023 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: 1701839589 Database = /dev/shm/rModeler.4fdqsM/GCA_949152265.1_fPhoPho1.1 - Sequences = 125 - Bases = 950498056 - N50 = 37204025 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52167619-55893807 |* [ 2 ] 48441432-52167619 | [ 1 ] 44715245-48441432 |* [ 3 ] 40989058-44715245 | [ 1 ] 37262871-40989058 |* [ 2 ] 33536684-37262871 |**** [ 9 ] 29810497-33536684 |* [ 3 ] 26084309-29810496 |* [ 3 ] 22358122-26084309 | [ 1 ] 18631935-22358122 | [ ] 14905748-18631935 | [ ] 11179561-14905748 | [ ] 7453374-11179561 | [ ] 3727187-7453374 | [ ] 1000-3727187 |************************************************** [ 100 ] Storage Throughput = excellent ( 1120.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013375 bp ( 40006357 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:23 (hh:mm:ss) Elapsed Time Round Time: 01:00:48 (hh:mm:ss) Elapsed Time : 1045 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 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14290 repeats masked totaling 2928569 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001448 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000248 bp After Masking: 6374155 bp Masked: 36.26 % -- Input Database Coverage: 10001448 bp out of 950498056 bp ( 1.05 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 12730 HSPs Collected Number of families returned by RECON: 1645 Round Time: 00:07:56 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43470 repeats masked totaling 8966726 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011918 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30006100 bp After Masking: 18872184 bp Masked: 37.11 % -- Input Database Coverage: 40013366 bp out of 950498056 bp ( 4.21 % ) Sampling Time: 00:06:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:29:12 (hh:mm:ss) Elapsed Time, 67824 HSPs Collected Number of families returned by RECON: 5735 Round Time: 00:38:05 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142163 repeats masked totaling 28291676 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047313 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90033313 bp After Masking: 54289998 bp Masked: 39.70 % -- Input Database Coverage: 130060679 bp out of 950498056 bp ( 13.68 % ) Sampling Time: 00:19:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:12:48 (hh:mm:ss) Elapsed Time, 529833 HSPs Collected Number of families returned by RECON: 16310 Round Time: 03:51:27 (hh:mm:ss) Elapsed Time : 681 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 517421 repeats masked totaling 105091851 bp(s). - TE Masking time 00:18:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057397 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270007406 bp After Masking: 142370648 bp Masked: 47.27 % -- Input Database Coverage: 400118076 bp out of 950498056 bp ( 42.10 % ) Sampling Time: 01:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 23:17:47 (hh:mm:ss) Elapsed Time, 1143901 HSPs Collected Number of families returned by RECON: 45113 Round Time: 26:01:55 (hh:mm:ss) Elapsed Time : 1591 families discovered. RepeatScout/RECON discovery complete: 3474 families found Classification Time: 02:35:35 (hh:mm:ss) Elapsed Time Program Time: 34:15:46 (hh:mm:ss) Elapsed Time