RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xEG2OU/RM_1255931.FriFeb142046172025 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: 1739594777 Database = /dev/shm/rModeler.xEG2OU/GCA_009767595.1_ASM976759v1 - Sequences = 30040 - Bases = 935067369 - N50 = 381704 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1786492-1914085 | [ 1 ] 1658900-1786492 | [ 1 ] 1531308-1658900 | [ 1 ] 1403715-1531307 | [ ] 1276123-1403715 | [ 7 ] 1148531-1276123 | [ 12 ] 1020938-1148530 | [ 24 ] 893346-1020938 | [ 27 ] 765754-893346 | [ 67 ] 638161-765753 | [ 119 ] 510569-638161 | [ 179 ] 382977-510569 | [ 329 ] 255384-382976 | [ 550 ] 127792-255384 |* [ 948 ] 200-127792 |************************************************** [ 27775 ] Storage Throughput = excellent ( 1890.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41539465 bp ( 40019440 non ambiguous ) - Num Contigs Represented = 2038 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:06 (hh:mm:ss) Elapsed Time Round Time: 00:08:56 (hh:mm:ss) Elapsed Time : 181 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 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5771 repeats masked totaling 581108 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10429543 bp Num Contigs Represented = 526 Non ambiguous bp: Initial: 10028209 bp After Masking: 8903330 bp Masked: 11.22 % -- Input Database Coverage: 10429543 bp out of 935067369 bp ( 1.12 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 147696 Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 18940 HSPs Collected Number of families returned by RECON: 1571 Round Time: 00:05:03 (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 : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23869 repeats masked totaling 3376081 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31151474 bp Num Contigs Represented = 1584 Non ambiguous bp: Initial: 30028353 bp After Masking: 25110301 bp Masked: 16.38 % -- Input Database Coverage: 41581017 bp out of 935067369 bp ( 4.45 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1468041 Comparison Time: 00:15:09 (hh:mm:ss) Elapsed Time, 24755 HSPs Collected Number of families returned by RECON: 4259 Round Time: 00:17:07 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76108 repeats masked totaling 10819935 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 93164913 bp Num Contigs Represented = 4121 Non ambiguous bp: Initial: 90001677 bp After Masking: 74259844 bp Masked: 17.49 % -- Input Database Coverage: 134745930 bp out of 935067369 bp ( 14.41 % ) Sampling Time: 00:04:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 12427605 Comparison Time: 01:21:52 (hh:mm:ss) Elapsed Time, 190363 HSPs Collected Number of families returned by RECON: 18596 Round Time: 01:33:04 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 255396 repeats masked totaling 38947799 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 279373525 bp Num Contigs Represented = 10685 Non ambiguous bp: Initial: 270027347 bp After Masking: 216490736 bp Masked: 19.83 % -- Input Database Coverage: 414119455 bp out of 935067369 bp ( 44.29 % ) Sampling Time: 00:15:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 116792686 Comparison Time: 09:17:01 (hh:mm:ss) Elapsed Time, 989447 HSPs Collected Number of families returned by RECON: 82511 Round Time: 10:24:32 (hh:mm:ss) Elapsed Time : 824 families discovered. RepeatScout/RECON discovery complete: 1288 families found Classification Time: 00:48:50 (hh:mm:ss) Elapsed Time Program Time: 13:17:32 (hh:mm:ss) Elapsed Time