RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.lVffJu/RM_2388727.ThuDec52232002024 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: 1733466719 Database = /scratch/tmp/rModeler.lVffJu/GCA_964199725.1_bLarMic1.1_alternate_haplotype - Sequences = 4673 - Bases = 1288335985 - N50 = 944478 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 5596476-5996020 | [ 2 ] 5196933-5596476 | [ ] 4797390-5196933 | [ 3 ] 4397847-4797390 | [ 1 ] 3998304-4397847 | [ ] 3598760-3998303 | [ 4 ] 3199217-3598760 | [ 5 ] 2799674-3199217 | [ 13 ] 2400131-2799674 | [ 21 ] 2000588-2400131 | [ 39 ] 1601044-2000587 | [ 66 ] 1201501-1601044 |* [ 124 ] 801958-1201501 |** [ 216 ] 402415-801958 |****** [ 489 ] 2872-402415 |************************************************** [ 3690 ] Storage Throughput = excellent ( 1476.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020013 bp ( 40020013 non ambiguous ) - Num Contigs Represented = 764 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:14 (hh:mm:ss) Elapsed Time Round Time: 00:10:36 (hh:mm:ss) Elapsed Time : 64 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 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1771 repeats masked totaling 598686 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021169 bp Num Contigs Represented = 241 Non ambiguous bp: Initial: 10021169 bp After Masking: 8936048 bp Masked: 10.83 % -- Input Database Coverage: 10021169 bp out of 1288335985 bp ( 0.78 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34980 Comparison Time: 00:11:08 (hh:mm:ss) Elapsed Time, 35601 HSPs Collected Number of families returned by RECON: 217 Round Time: 00:11:29 (hh:mm:ss) Elapsed Time : 2 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 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5503 repeats masked totaling 1898346 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038802 bp Num Contigs Represented = 621 Non ambiguous bp: Initial: 30038802 bp After Masking: 26438616 bp Masked: 11.99 % -- Input Database Coverage: 40059971 bp out of 1288335985 bp ( 3.11 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 325221 Comparison Time: 01:07:32 (hh:mm:ss) Elapsed Time, 640052 HSPs Collected Number of families returned by RECON: 1185 Round Time: 01:09:16 (hh:mm:ss) Elapsed Time : 17 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 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18280 repeats masked totaling 7036046 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008768 bp Num Contigs Represented = 1297 Non ambiguous bp: Initial: 90008768 bp After Masking: 77978912 bp Masked: 13.37 % -- Input Database Coverage: 130068739 bp out of 1288335985 bp ( 10.10 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2948806 Comparison Time: 06:08:11 (hh:mm:ss) Elapsed Time, 5201594 HSPs Collected Number of families returned by RECON: 6651 Round Time: 06:44:38 (hh:mm:ss) Elapsed Time : 50 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 00:06:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65937 repeats masked totaling 25409593 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028740 bp Num Contigs Represented = 2275 Non ambiguous bp: Initial: 270028740 bp After Masking: 228703031 bp Masked: 15.30 % -- Input Database Coverage: 400097479 bp out of 1288335985 bp ( 31.06 % ) Sampling Time: 00:08:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26024505 Comparison Time: 43:33:26 (hh:mm:ss) Elapsed Time, 50398695 HSPs Collected Number of families returned by RECON: 41177 Round Time: 44:04:37 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatScout/RECON discovery complete: 332 families found Classification Time: 00:16:18 (hh:mm:ss) Elapsed Time Program Time: 52:36:54 (hh:mm:ss) Elapsed Time