RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.kRScHY/RM_2392645.MonDec90746562024 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: 1733759215 Database = /scratch/tmp/rModeler.kRScHY/GCA_043161795.1_mMacNem.hap2 - Sequences = 233 - Bases = 2963967802 - N50 = 178996168 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 218744788-234368445 | [ 1 ] 203121131-218744788 | [ 1 ] 187497474-203121131 | [ 3 ] 171873817-187497474 | [ 2 ] 156250160-171873817 | [ ] 140626503-156250160 | [ 3 ] 125002846-140626503 | [ 2 ] 109379189-125002846 | [ 3 ] 93755532-109379189 | [ 1 ] 78131875-93755532 | [ 3 ] 62508218-78131875 | [ 1 ] 46884561-62508218 | [ ] 31260904-46884561 | [ ] 15637247-31260904 | [ ] 13590-15637247 |************************************************** [ 213 ] Storage Throughput = excellent ( 1539.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007541 bp ( 40007141 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:21 (hh:mm:ss) Elapsed Time Round Time: 00:12:56 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12588 repeats masked totaling 2902652 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001654 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10001454 bp After Masking: 6307924 bp Masked: 36.93 % -- Input Database Coverage: 10001654 bp out of 2963967802 bp ( 0.34 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:36 (hh:mm:ss) Elapsed Time, 5513 HSPs Collected Number of families returned by RECON: 716 Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40956 repeats masked totaling 9500826 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005886 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30005686 bp After Masking: 18214886 bp Masked: 39.30 % -- Input Database Coverage: 40007540 bp out of 2963967802 bp ( 1.35 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:11:04 (hh:mm:ss) Elapsed Time, 32869 HSPs Collected Number of families returned by RECON: 2286 Round Time: 00:13:56 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129780 repeats masked totaling 29687127 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018454 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90016954 bp After Masking: 51522434 bp Masked: 42.76 % -- Input Database Coverage: 130025994 bp out of 2963967802 bp ( 4.39 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:05:18 (hh:mm:ss) Elapsed Time, 339606 HSPs Collected Number of families returned by RECON: 7263 Round Time: 01:14:53 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 430414 repeats masked totaling 98001765 bp(s). - TE Masking time 00:02:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021261 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 270017025 bp After Masking: 149189067 bp Masked: 44.75 % -- Input Database Coverage: 400047255 bp out of 2963967802 bp ( 13.50 % ) Sampling Time: 00:25:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 07:34:25 (hh:mm:ss) Elapsed Time, 655269 HSPs Collected Number of families returned by RECON: 29809 Round Time: 08:10:10 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatScout/RECON discovery complete: 922 families found Classification Time: 00:22:50 (hh:mm:ss) Elapsed Time Program Time: 10:18:32 (hh:mm:ss) Elapsed Time