RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.c7uPoG/RM_31853.WedJul30424352024 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: 1720005874 Database = /dev/shm/rModeler.c7uPoG/GCA_902148815.1_fMyrMur1.1_alternate_haplotype - Sequences = 2193 - Bases = 819084930 - N50 = 612581 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 5509356-5902824 | [ 1 ] 5115888-5509355 | [ ] 4722421-5115888 | [ ] 4328953-4722420 | [ ] 3935486-4328953 | [ 1 ] 3542018-3935485 | [ 2 ] 3148550-3542017 | [ 3 ] 2755083-3148550 | [ 9 ] 2361615-2755082 | [ 6 ] 1968148-2361615 | [ 17 ] 1574680-1968147 | [ 22 ] 1181212-1574679 |* [ 45 ] 787745-1181212 |**** [ 135 ] 394277-787744 |************** [ 450 ] 810-394277 |************************************************** [ 1502 ] Storage Throughput = good ( 960.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027674 bp ( 40027198 non ambiguous ) - Num Contigs Represented = 686 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:09 (hh:mm:ss) Elapsed Time Round Time: 00:24:52 (hh:mm:ss) Elapsed Time : 470 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6778 repeats masked totaling 1126376 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011710 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 10011710 bp After Masking: 8589432 bp Masked: 14.21 % -- Input Database Coverage: 10011710 bp out of 819084930 bp ( 1.22 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35245 Comparison Time: 00:07:22 (hh:mm:ss) Elapsed Time, 12016 HSPs Collected Number of families returned by RECON: 2355 Round Time: 00:08:31 (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 : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21918 repeats masked totaling 3670993 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015884 bp Num Contigs Represented = 553 Non ambiguous bp: Initial: 30015408 bp After Masking: 25435355 bp Masked: 15.26 % -- Input Database Coverage: 40027594 bp out of 819084930 bp ( 4.89 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 310866 Comparison Time: 00:45:15 (hh:mm:ss) Elapsed Time, 86856 HSPs Collected Number of families returned by RECON: 8672 Round Time: 00:51:42 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86914 repeats masked totaling 14542849 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90000976 bp Num Contigs Represented = 1176 Non ambiguous bp: Initial: 90000976 bp After Masking: 72892114 bp Masked: 19.01 % -- Input Database Coverage: 130028570 bp out of 819084930 bp ( 15.87 % ) Sampling Time: 00:07:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2795430 Comparison Time: 05:45:01 (hh:mm:ss) Elapsed Time, 386482 HSPs Collected Number of families returned by RECON: 27003 Round Time: 06:22:08 (hh:mm:ss) Elapsed Time : 701 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 362020 repeats masked totaling 62472357 bp(s). - TE Masking time 00:18:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013424 bp Num Contigs Represented = 1801 Non ambiguous bp: Initial: 270013392 bp After Masking: 199629504 bp Masked: 26.07 % -- Input Database Coverage: 400041994 bp out of 819084930 bp ( 48.84 % ) Sampling Time: 00:34:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25379250 Comparison Time: 43:25:15 (hh:mm:ss) Elapsed Time, 1117252 HSPs Collected Number of families returned by RECON: 86274 Round Time: 48:01:02 (hh:mm:ss) Elapsed Time : 1696 families discovered. RepeatScout/RECON discovery complete: 3056 families found Classification Time: 02:24:08 (hh:mm:ss) Elapsed Time Program Time: 58:12:23 (hh:mm:ss) Elapsed Time