RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Q39XxL/RM_9209.ThuDec71007592023 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: 1701972478 Database = /dev/shm/rModeler.Q39XxL/GCA_949987515.1_mDelDel1.1 - Sequences = 631 - Bases = 2663533373 - N50 = 110534049 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172543118-184867555 | [ 3 ] 160218681-172543118 | [ ] 147894244-160218681 | [ ] 135569807-147894244 | [ 2 ] 123245370-135569807 | [ 1 ] 110920933-123245370 | [ 2 ] 98596496-110920933 | [ 4 ] 86272059-98596496 | [ 4 ] 73947622-86272059 | [ 3 ] 61623185-73947622 | [ ] 49298748-61623185 | [ 2 ] 36974311-49298748 | [ ] 24649874-36974311 | [ 1 ] 12325437-24649874 | [ ] 1000-12325437 |************************************************** [ 609 ] Storage Throughput = excellent ( 1160.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033162 bp ( 40030562 non ambiguous ) - Num Contigs Represented = 122 - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:23 (hh:mm:ss) Elapsed Time Round Time: 00:42:05 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8676 repeats masked totaling 2951814 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010488 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10009688 bp After Masking: 6758860 bp Masked: 32.48 % -- Input Database Coverage: 10010488 bp out of 2663533373 bp ( 0.38 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:16 (hh:mm:ss) Elapsed Time, 91226 HSPs Collected Number of families returned by RECON: 838 Round Time: 00:10:04 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32923 repeats masked totaling 10927392 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022594 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 30020794 bp After Masking: 18350918 bp Masked: 38.87 % -- Input Database Coverage: 40033082 bp out of 2663533373 bp ( 1.50 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:28:36 (hh:mm:ss) Elapsed Time, 28951 HSPs Collected Number of families returned by RECON: 1964 Round Time: 00:33:39 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104542 repeats masked totaling 35168568 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027038 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 90018838 bp After Masking: 52770270 bp Masked: 41.38 % -- Input Database Coverage: 130060120 bp out of 2663533373 bp ( 4.88 % ) Sampling Time: 00:11:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:11:33 (hh:mm:ss) Elapsed Time, 74355 HSPs Collected Number of families returned by RECON: 6917 Round Time: 03:26:07 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 345360 repeats masked totaling 110563917 bp(s). - TE Masking time 00:04:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059149 bp Num Contigs Represented = 329 Non ambiguous bp: Initial: 270039889 bp After Masking: 152983946 bp Masked: 43.35 % -- Input Database Coverage: 400119269 bp out of 2663533373 bp ( 15.02 % ) Sampling Time: 00:36:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 21:57:11 (hh:mm:ss) Elapsed Time, 409289 HSPs Collected Number of families returned by RECON: 29585 Round Time: 22:56:25 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatScout/RECON discovery complete: 777 families found Classification Time: 00:27:59 (hh:mm:ss) Elapsed Time Program Time: 28:16:19 (hh:mm:ss) Elapsed Time