RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.usFFt2/RM_22031.FriJul190930242024 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: 1721406619 Database = /dev/shm/rModeler.usFFt2/GCF_013358895.1_ZZ_aureus - Sequences = 304 - Bases = 1005575223 - N50 = 41599371 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 125429685-134388234 | [ 1 ] 116471136-125429684 | [ ] 107512587-116471135 | [ ] 98554038-107512586 | [ ] 89595489-98554037 | [ ] 80636940-89595488 | [ ] 71678391-80636939 | [ ] 62719843-71678391 | [ 1 ] 53761294-62719842 | [ ] 44802745-53761293 | [ 1 ] 35844196-44802744 |*** [ 17 ] 26885647-35844195 | [ 2 ] 17927098-26885646 | [ ] 8968549-17927097 | [ ] 10001-8968549 |************************************************** [ 282 ] Storage Throughput = good ( 984.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038923 bp ( 40024344 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:03 (hh:mm:ss) Elapsed Time Round Time: 00:36:27 (hh:mm:ss) Elapsed Time : 728 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11573 repeats masked totaling 2959262 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010784 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10007012 bp After Masking: 6841761 bp Masked: 31.63 % -- Input Database Coverage: 10010784 bp out of 1005575223 bp ( 1.00 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:19:58 (hh:mm:ss) Elapsed Time, 8909 HSPs Collected Number of families returned by RECON: 1288 Round Time: 00:21:58 (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 : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34870 repeats masked totaling 8611689 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028059 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30017252 bp After Masking: 20847802 bp Masked: 30.55 % -- Input Database Coverage: 40038843 bp out of 1005575223 bp ( 3.98 % ) Sampling Time: 00:03:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:17:58 (hh:mm:ss) Elapsed Time, 48430 HSPs Collected Number of families returned by RECON: 4562 Round Time: 01:24:34 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110665 repeats masked totaling 25796179 bp(s). - TE Masking time 00:03:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045237 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 90018691 bp After Masking: 62700820 bp Masked: 30.35 % -- Input Database Coverage: 130084080 bp out of 1005575223 bp ( 12.94 % ) Sampling Time: 00:10:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 06:37:47 (hh:mm:ss) Elapsed Time, 254807 HSPs Collected Number of families returned by RECON: 14763 Round Time: 07:15:18 (hh:mm:ss) Elapsed Time : 448 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 399783 repeats masked totaling 93705076 bp(s). - TE Masking time 00:16:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270105608 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 270036392 bp After Masking: 171613982 bp Masked: 36.45 % -- Input Database Coverage: 400189688 bp out of 1005575223 bp ( 39.80 % ) Sampling Time: 00:38:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 30:12:17 (hh:mm:ss) Elapsed Time, 735435 HSPs Collected Number of families returned by RECON: 51639 Round Time: 32:30:45 (hh:mm:ss) Elapsed Time : 1144 families discovered. RepeatScout/RECON discovery complete: 2425 families found Classification Time: 02:22:04 (hh:mm:ss) Elapsed Time Program Time: 44:31:06 (hh:mm:ss) Elapsed Time