RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Oz3xsz/RM_3411213.ThuMar140654132024 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: 1710424451 Database = /dev/shm/rModeler.Oz3xsz/GCA_035125265.1_rCanAsp1.hap1 - Sequences = 180 - Bases = 1529331567 - N50 = 263517667 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 316269260-338859053 | [ 1 ] 293679467-316269259 | [ ] 271089674-293679466 | [ ] 248499882-271089674 | [ 1 ] 225910089-248499881 | [ ] 203320296-225910088 | [ 1 ] 180730503-203320295 | [ ] 158140711-180730503 | [ ] 135550918-158140710 | [ ] 112961125-135550917 | [ 2 ] 90371332-112961124 | [ 2 ] 67781540-90371332 | [ 2 ] 45191747-67781539 | [ ] 22601954-45191746 | [ 2 ] 12162-22601954 |************************************************** [ 169 ] Storage Throughput = excellent ( 1248.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011959 bp ( 40011759 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:46 (hh:mm:ss) Elapsed Time Round Time: 00:23:44 (hh:mm:ss) Elapsed Time : 341 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9616 repeats masked totaling 2856292 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009785 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10009785 bp After Masking: 7058073 bp Masked: 29.49 % -- Input Database Coverage: 10009785 bp out of 1529331567 bp ( 0.65 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 9387 HSPs Collected Number of families returned by RECON: 1202 Round Time: 00:07:37 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33025 repeats masked totaling 9391021 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002094 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001894 bp After Masking: 20238954 bp Masked: 32.54 % -- Input Database Coverage: 40011879 bp out of 1529331567 bp ( 2.62 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:05 (hh:mm:ss) Elapsed Time, 30048 HSPs Collected Number of families returned by RECON: 3557 Round Time: 00:33:12 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108286 repeats masked totaling 29613561 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020450 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90018850 bp After Masking: 58891851 bp Masked: 34.58 % -- Input Database Coverage: 130032329 bp out of 1529331567 bp ( 8.50 % ) Sampling Time: 00:12:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:03:36 (hh:mm:ss) Elapsed Time, 171732 HSPs Collected Number of families returned by RECON: 12348 Round Time: 03:23:23 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383518 repeats masked totaling 100182140 bp(s). - TE Masking time 00:07:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043566 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270039566 bp After Masking: 166146629 bp Masked: 38.47 % -- Input Database Coverage: 400075895 bp out of 1529331567 bp ( 26.16 % ) Sampling Time: 00:42:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 20:06:14 (hh:mm:ss) Elapsed Time, 628304 HSPs Collected Number of families returned by RECON: 43917 Round Time: 21:34:52 (hh:mm:ss) Elapsed Time : 743 families discovered. RepeatScout/RECON discovery complete: 1531 families found Classification Time: 01:03:43 (hh:mm:ss) Elapsed Time Program Time: 27:06:31 (hh:mm:ss) Elapsed Time