RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.guVPhu/RM_3473127.SunApr202347442025 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: 1745218061 Database = /dev/shm/rModeler.guVPhu/GCA_024256435.1_CGAR_Hap1 - Sequences = 119 - Bases = 972641408 - N50 = 34153891 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48324120-51775064 |* [ 2 ] 44873176-48324120 | [ 1 ] 41422232-44873176 |* [ 2 ] 37971288-41422232 |** [ 4 ] 34520344-37971288 | [ 1 ] 31069400-34520344 |*** [ 6 ] 27618456-31069400 |*** [ 6 ] 24167512-27618456 |** [ 4 ] 20716568-24167512 | [ 1 ] 17265624-20716568 | [ 1 ] 13814680-17265624 | [ ] 10363736-13814680 | [ ] 6912792-10363736 | [ ] 3461848-6912792 | [ ] 10904-3461848 |************************************************** [ 91 ] Storage Throughput = excellent ( 1703.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005437 bp ( 40004937 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:32 (hh:mm:ss) Elapsed Time Round Time: 00:09:49 (hh:mm:ss) Elapsed Time : 658 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14955 repeats masked totaling 2872368 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026921 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10026921 bp After Masking: 6749255 bp Masked: 32.69 % -- Input Database Coverage: 10026921 bp out of 972641408 bp ( 1.03 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 7861 HSPs Collected Number of families returned by RECON: 1485 Round Time: 00:03:52 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46277 repeats masked totaling 8711571 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018584 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30018084 bp After Masking: 19840430 bp Masked: 33.91 % -- Input Database Coverage: 40045505 bp out of 972641408 bp ( 4.12 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:13:35 (hh:mm:ss) Elapsed Time, 57349 HSPs Collected Number of families returned by RECON: 5175 Round Time: 00:16:22 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151738 repeats masked totaling 28621164 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027430 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90026592 bp After Masking: 57723502 bp Masked: 35.88 % -- Input Database Coverage: 130072935 bp out of 972641408 bp ( 13.37 % ) Sampling Time: 00:06:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:21:01 (hh:mm:ss) Elapsed Time, 323596 HSPs Collected Number of families returned by RECON: 15900 Round Time: 01:34:54 (hh:mm:ss) Elapsed Time : 444 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 523897 repeats masked totaling 100115203 bp(s). - TE Masking time 00:04:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040906 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270038773 bp After Masking: 158483789 bp Masked: 41.31 % -- Input Database Coverage: 400113841 bp out of 972641408 bp ( 41.14 % ) Sampling Time: 00:20:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 09:16:52 (hh:mm:ss) Elapsed Time, 1021813 HSPs Collected Number of families returned by RECON: 53180 Round Time: 10:11:43 (hh:mm:ss) Elapsed Time : 1062 families discovered. RepeatScout/RECON discovery complete: 2308 families found Classification Time: 00:50:34 (hh:mm:ss) Elapsed Time Program Time: 13:07:14 (hh:mm:ss) Elapsed Time