RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FbDVlq/RM_29414.FriMay121000012023 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: 1683910800 Database = /dev/shm/rModeler.FbDVlq/GCA_900246225.5_fAstCal1.3 - Sequences = 249 - Bases = 880445568 - N50 = 38678279 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 63839031-68397778 | [ 1 ] 59280285-63839031 | [ ] 54721538-59280284 | [ ] 50162792-54721538 | [ 1 ] 45604046-50162792 | [ ] 41045299-45604045 | [ 3 ] 36486553-41045299 |* [ 7 ] 31927806-36486552 |* [ 7 ] 27369060-31927806 | [ 2 ] 22810314-27369060 | [ 1 ] 18251567-22810313 | [ ] 13692821-18251567 | [ ] 9134074-13692820 | [ ] 4575328-9134074 | [ ] 16582-4575328 |************************************************** [ 227 ] Storage Throughput = excellent ( 1209.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40200503 bp ( 40035311 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:18 (hh:mm:ss) Elapsed Time Round Time: 00:26:39 (hh:mm:ss) Elapsed Time : 614 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 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10262 repeats masked totaling 2559422 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10064679 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10024479 bp After Masking: 7338949 bp Masked: 26.79 % -- Input Database Coverage: 10064679 bp out of 880445568 bp ( 1.14 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:10 (hh:mm:ss) Elapsed Time, 6518 HSPs Collected Number of families returned by RECON: 1311 Round Time: 00:08:29 (hh:mm:ss) Elapsed Time : 12 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 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31020 repeats masked totaling 7186407 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30135815 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30010823 bp After Masking: 22497605 bp Masked: 25.04 % -- Input Database Coverage: 40200494 bp out of 880445568 bp ( 4.57 % ) Sampling Time: 00:02:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:35:50 (hh:mm:ss) Elapsed Time, 41702 HSPs Collected Number of families returned by RECON: 4164 Round Time: 00:40:11 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 103750 repeats masked totaling 23969512 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90156647 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90034879 bp After Masking: 65083946 bp Masked: 27.71 % -- Input Database Coverage: 130357141 bp out of 880445568 bp ( 14.81 % ) Sampling Time: 00:07:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:46:11 (hh:mm:ss) Elapsed Time, 211267 HSPs Collected Number of families returned by RECON: 14335 Round Time: 04:06:48 (hh:mm:ss) Elapsed Time : 371 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 00:10:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361970 repeats masked totaling 84156253 bp(s). - TE Masking time 00:12:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270452409 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270037245 bp After Masking: 182442415 bp Masked: 32.44 % -- Input Database Coverage: 400809550 bp out of 880445568 bp ( 45.52 % ) Sampling Time: 00:29:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 27:54:02 (hh:mm:ss) Elapsed Time, 746585 HSPs Collected Number of families returned by RECON: 53930 Round Time: 29:55:35 (hh:mm:ss) Elapsed Time : 1053 families discovered. RepeatScout/RECON discovery complete: 2145 families found Classification Time: 02:11:58 (hh:mm:ss) Elapsed Time Program Time: 37:29:40 (hh:mm:ss) Elapsed Time