RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GEw6dm/RM_21101.TueMay161958142023 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: 1684292293 Database = /dev/shm/rModeler.GEw6dm/GCF_027595985.1_mSorAra2.pri - Sequences = 65 - Bases = 2405993548 Storage Throughput = excellent ( 1119.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40120775 bp ( 40027857 non ambiguous ) - Num Contigs Represented = 13 - Sequence extraction : 00:06:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:37 (hh:mm:ss) Elapsed Time Round Time: 00:33:21 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16134 repeats masked totaling 3286947 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10079982 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10034313 bp After Masking: 6540750 bp Masked: 34.82 % -- Input Database Coverage: 10079982 bp out of 2405993548 bp ( 0.42 % ) Sampling Time: 00:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 4688 HSPs Collected Number of families returned by RECON: 620 Round Time: 00:09:56 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52005 repeats masked totaling 10238955 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30080793 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 30033544 bp After Masking: 19080968 bp Masked: 36.47 % -- Input Database Coverage: 40160775 bp out of 2405993548 bp ( 1.67 % ) Sampling Time: 00:06:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:33:13 (hh:mm:ss) Elapsed Time, 14061 HSPs Collected Number of families returned by RECON: 2030 Round Time: 00:40:50 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168497 repeats masked totaling 32363609 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90531008 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 90000113 bp After Masking: 55639233 bp Masked: 38.18 % -- Input Database Coverage: 130691783 bp out of 2405993548 bp ( 5.43 % ) Sampling Time: 00:20:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:25:30 (hh:mm:ss) Elapsed Time, 62159 HSPs Collected Number of families returned by RECON: 6421 Round Time: 03:49:12 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 537085 repeats masked totaling 101328546 bp(s). - TE Masking time 00:06:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271518197 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270029668 bp After Masking: 162386330 bp Masked: 39.86 % -- Input Database Coverage: 402209980 bp out of 2405993548 bp ( 16.72 % ) Sampling Time: 01:02:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 26:00:56 (hh:mm:ss) Elapsed Time, 182437 HSPs Collected Number of families returned by RECON: 28228 Round Time: 27:26:07 (hh:mm:ss) Elapsed Time : 353 families discovered. RepeatScout/RECON discovery complete: 750 families found Classification Time: 00:30:48 (hh:mm:ss) Elapsed Time Program Time: 33:10:14 (hh:mm:ss) Elapsed Time