RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.oLTBGX/RM_1817341.SatNov161506032024 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: 1731798363 Database = /scratch/tmp/rModeler.oLTBGX/GCA_964106645.2_rPodPit1.hap1.2 - Sequences = 336 - Bases = 1515373509 - N50 = 99259010 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130365566-139677321 | [ 1 ] 121053811-130365565 | [ 2 ] 111742056-121053810 | [ ] 102430302-111742056 | [ 1 ] 93118547-102430301 | [ 2 ] 83806792-93118546 | [ 2 ] 74495037-83806791 | [ 2 ] 65183283-74495037 | [ ] 55871528-65183282 | [ 2 ] 46559773-55871527 | [ 3 ] 37248018-46559772 | [ 4 ] 27936264-37248018 | [ ] 18624509-27936263 | [ ] 9312754-18624508 | [ 1 ] 1000-9312754 |************************************************** [ 316 ] Storage Throughput = excellent ( 1514.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019111 bp ( 40010311 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:48 (hh:mm:ss) Elapsed Time Round Time: 00:11:06 (hh:mm:ss) Elapsed Time : 578 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17743 repeats masked totaling 3267566 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026898 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10025498 bp After Masking: 6644720 bp Masked: 33.72 % -- Input Database Coverage: 10026898 bp out of 1515373509 bp ( 0.66 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 9913 HSPs Collected Number of families returned by RECON: 1352 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56307 repeats masked totaling 10699168 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032255 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30024855 bp After Masking: 18913866 bp Masked: 37.01 % -- Input Database Coverage: 40059153 bp out of 1515373509 bp ( 2.64 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:12:42 (hh:mm:ss) Elapsed Time, 45536 HSPs Collected Number of families returned by RECON: 4283 Round Time: 00:14:49 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179449 repeats masked totaling 33613376 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90051421 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90032453 bp After Masking: 54669083 bp Masked: 39.28 % -- Input Database Coverage: 130110574 bp out of 1515373509 bp ( 8.59 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:14:04 (hh:mm:ss) Elapsed Time, 183223 HSPs Collected Number of families returned by RECON: 13798 Round Time: 01:22:51 (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 : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 607696 repeats masked totaling 111252437 bp(s). - TE Masking time 00:03:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270080285 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 270027285 bp After Masking: 153518184 bp Masked: 43.15 % -- Input Database Coverage: 400190859 bp out of 1515373509 bp ( 26.41 % ) Sampling Time: 00:14:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 07:34:06 (hh:mm:ss) Elapsed Time, 459633 HSPs Collected Number of families returned by RECON: 47385 Round Time: 08:14:46 (hh:mm:ss) Elapsed Time : 1046 families discovered. RepeatScout/RECON discovery complete: 2216 families found Classification Time: 00:34:30 (hh:mm:ss) Elapsed Time Program Time: 10:41:40 (hh:mm:ss) Elapsed Time