RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9fewqz/RM_169378.FriDec82143272023 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: 1702100605 Database = /dev/shm/rModeler.9fewqz/GCA_951804945.1_rPodCre2.1 - Sequences = 51 - Bases = 1507627055 Storage Throughput = excellent ( 1255.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024382 bp ( 40023782 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:28 (hh:mm:ss) Elapsed Time Round Time: 00:18:06 (hh:mm:ss) Elapsed Time : 546 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17487 repeats masked totaling 3370434 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000436 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000236 bp After Masking: 6446548 bp Masked: 35.54 % -- Input Database Coverage: 10000436 bp out of 1507627055 bp ( 0.66 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 9169 HSPs Collected Number of families returned by RECON: 1251 Round Time: 00:07:02 (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 : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55131 repeats masked totaling 10413045 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023939 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30023539 bp After Masking: 18907999 bp Masked: 37.02 % -- Input Database Coverage: 40024375 bp out of 1507627055 bp ( 2.65 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:14 (hh:mm:ss) Elapsed Time, 40775 HSPs Collected Number of families returned by RECON: 4213 Round Time: 00:28:49 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 180020 repeats masked totaling 32848582 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002750 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90002150 bp After Masking: 54861350 bp Masked: 39.04 % -- Input Database Coverage: 130027125 bp out of 1507627055 bp ( 8.62 % ) Sampling Time: 00:06:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:09:12 (hh:mm:ss) Elapsed Time, 188120 HSPs Collected Number of families returned by RECON: 13937 Round Time: 02:24:08 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 606041 repeats masked totaling 109731013 bp(s). - TE Masking time 00:04:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038111 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270036511 bp After Masking: 153928929 bp Masked: 43.00 % -- Input Database Coverage: 400065236 bp out of 1507627055 bp ( 26.54 % ) Sampling Time: 00:22:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 14:42:45 (hh:mm:ss) Elapsed Time, 527117 HSPs Collected Number of families returned by RECON: 48391 Round Time: 15:47:03 (hh:mm:ss) Elapsed Time : 1041 families discovered. RepeatScout/RECON discovery complete: 2160 families found Classification Time: 00:44:24 (hh:mm:ss) Elapsed Time Program Time: 19:49:32 (hh:mm:ss) Elapsed Time