RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sp4W7n/RM_1855825.TueApr220817132025 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: 1745335033 Database = /dev/shm/rModeler.sp4W7n/GCA_965140285.1_rLepKem1.hap1 - Sequences = 54 - Bases = 2219022919 Storage Throughput = excellent ( 1835.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038963 bp ( 40038163 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:52 (hh:mm:ss) Elapsed Time Round Time: 00:11:24 (hh:mm:ss) Elapsed Time : 503 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (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... 12679 repeats masked totaling 2871164 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000825 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000825 bp After Masking: 6929943 bp Masked: 30.71 % -- Input Database Coverage: 10000825 bp out of 2219022919 bp ( 0.45 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 13502 HSPs Collected Number of families returned by RECON: 1678 Round Time: 00:03:46 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (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... 43402 repeats masked totaling 9573168 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038120 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30037320 bp After Masking: 20086523 bp Masked: 33.13 % -- Input Database Coverage: 40038945 bp out of 2219022919 bp ( 1.80 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:00 (hh:mm:ss) Elapsed Time, 62455 HSPs Collected Number of families returned by RECON: 4983 Round Time: 00:15:06 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149787 repeats masked totaling 32195369 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033781 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90032381 bp After Masking: 56576445 bp Masked: 37.16 % -- Input Database Coverage: 130072726 bp out of 2219022919 bp ( 5.86 % ) Sampling Time: 00:06:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:07:46 (hh:mm:ss) Elapsed Time, 221213 HSPs Collected Number of families returned by RECON: 13706 Round Time: 01:18:53 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 510773 repeats masked totaling 112234819 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017340 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270010340 bp After Masking: 153733123 bp Masked: 43.06 % -- Input Database Coverage: 400090066 bp out of 2219022919 bp ( 18.03 % ) Sampling Time: 00:21:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 07:27:29 (hh:mm:ss) Elapsed Time, 607272 HSPs Collected Number of families returned by RECON: 44855 Round Time: 08:14:27 (hh:mm:ss) Elapsed Time : 1029 families discovered. RepeatScout/RECON discovery complete: 2131 families found Classification Time: 00:39:11 (hh:mm:ss) Elapsed Time Program Time: 10:42:47 (hh:mm:ss) Elapsed Time