RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RQoACL/RM_374985.SatApr191855452025 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: 1745114145 Database = /dev/shm/rModeler.RQoACL/GCF_040182565.1_Taihu_goose_T2T_genome - Sequences = 75 - Bases = 1215354515 Storage Throughput = excellent ( 1710.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029976 bp ( 40029676 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:54 (hh:mm:ss) Elapsed Time Round Time: 00:10:12 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1753 repeats masked totaling 717092 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004626 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10004626 bp After Masking: 8748031 bp Masked: 12.56 % -- Input Database Coverage: 10004626 bp out of 1215354515 bp ( 0.82 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 467 HSPs Collected Number of families returned by RECON: 208 Round Time: 00:04:05 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5164 repeats masked totaling 2053589 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025270 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30024970 bp After Masking: 26525633 bp Masked: 11.65 % -- Input Database Coverage: 40029896 bp out of 1215354515 bp ( 3.29 % ) Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:15:38 (hh:mm:ss) Elapsed Time, 3814 HSPs Collected Number of families returned by RECON: 1330 Round Time: 00:18:11 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16976 repeats masked totaling 6516560 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004662 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90003962 bp After Masking: 79027278 bp Masked: 12.20 % -- Input Database Coverage: 130034558 bp out of 1215354515 bp ( 10.70 % ) Sampling Time: 00:07:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:40:38 (hh:mm:ss) Elapsed Time, 56675 HSPs Collected Number of families returned by RECON: 8213 Round Time: 01:52:31 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58467 repeats masked totaling 21987572 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031840 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270030240 bp After Masking: 235228289 bp Masked: 12.89 % -- Input Database Coverage: 400066398 bp out of 1215354515 bp ( 32.92 % ) Sampling Time: 00:20:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 12:38:03 (hh:mm:ss) Elapsed Time, 251618 HSPs Collected Number of families returned by RECON: 54739 Round Time: 13:16:35 (hh:mm:ss) Elapsed Time : 243 families discovered. RepeatScout/RECON discovery complete: 386 families found Classification Time: 00:16:28 (hh:mm:ss) Elapsed Time Program Time: 15:58:02 (hh:mm:ss) Elapsed Time