RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Y0m8zP/RM_19801.TueNov280800102023 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: 1701187210 Database = /dev/shm/rModeler.Y0m8zP/GCA_028017805.1_mBalRic1.hap1 - Sequences = 1039 - Bases = 2844045133 - N50 = 113157400 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 176360054-188956366 | [ 1 ] 163763742-176360053 | [ 1 ] 151167430-163763741 | [ ] 138571118-151167429 | [ 3 ] 125974806-138571117 | [ 2 ] 113378494-125974805 | [ 2 ] 100782182-113378493 | [ 5 ] 88185871-100782182 | [ 3 ] 75589559-88185870 | [ 3 ] 62993247-75589558 | [ ] 50396935-62993246 | [ 1 ] 37800623-50396934 | [ ] 25204311-37800622 | [ 1 ] 12607999-25204310 | [ ] 11688-12607999 |************************************************** [ 1017 ] Storage Throughput = excellent ( 1182.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41012590 bp ( 40012365 non ambiguous ) - Num Contigs Represented = 135 - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:50 (hh:mm:ss) Elapsed Time Round Time: 00:43:15 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9376 repeats masked totaling 2842322 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10133578 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10013578 bp After Masking: 6482602 bp Masked: 35.26 % -- Input Database Coverage: 10133578 bp out of 2844045133 bp ( 0.36 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 82908 HSPs Collected Number of families returned by RECON: 779 Round Time: 00:10:36 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35381 repeats masked totaling 10080922 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30919012 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 30038787 bp After Masking: 18703902 bp Masked: 37.73 % -- Input Database Coverage: 41052590 bp out of 2844045133 bp ( 1.44 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 304590 Comparison Time: 00:31:21 (hh:mm:ss) Elapsed Time, 251961 HSPs Collected Number of families returned by RECON: 2104 Round Time: 00:38:37 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112224 repeats masked totaling 31160589 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92151424 bp Num Contigs Represented = 241 Non ambiguous bp: Initial: 90031294 bp After Masking: 53623316 bp Masked: 40.44 % -- Input Database Coverage: 133204014 bp out of 2844045133 bp ( 4.68 % ) Sampling Time: 00:16:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2694681 Comparison Time: 03:10:45 (hh:mm:ss) Elapsed Time, 911167 HSPs Collected Number of families returned by RECON: 7312 Round Time: 03:31:36 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 380700 repeats masked totaling 101214110 bp(s). - TE Masking time 00:06:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275684331 bp Num Contigs Represented = 419 Non ambiguous bp: Initial: 270008243 bp After Masking: 155104369 bp Masked: 42.56 % -- Input Database Coverage: 408888345 bp out of 2844045133 bp ( 14.38 % ) Sampling Time: 00:51:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24071391 Comparison Time: 23:25:02 (hh:mm:ss) Elapsed Time, 5064855 HSPs Collected Number of families returned by RECON: 30971 Round Time: 24:43:37 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatScout/RECON discovery complete: 765 families found Classification Time: 00:34:53 (hh:mm:ss) Elapsed Time Program Time: 30:22:34 (hh:mm:ss) Elapsed Time