RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.OeCJ4s/RM_11742.ThuDec51304012024 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: 1733432640 Database = /scratch/tmp/rModeler.OeCJ4s/GCA_037038555.1_mRhyNas2.hap2 - Sequences = 38 - Bases = 2296372838 Storage Throughput = fair ( 612.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012548 bp ( 40012548 non ambiguous ) - Num Contigs Represented = 13 - Sequence extraction : 00:05:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:59 (hh:mm:ss) Elapsed Time Round Time: 00:35:37 (hh:mm:ss) Elapsed Time : 257 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10858 repeats masked totaling 3147357 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022345 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 10022345 bp After Masking: 6805937 bp Masked: 32.09 % -- Input Database Coverage: 10022345 bp out of 2296372838 bp ( 0.44 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 9005 HSPs Collected Number of families returned by RECON: 888 Round Time: 00:07:45 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35435 repeats masked totaling 9648455 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030123 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 30030123 bp After Masking: 20183299 bp Masked: 32.79 % -- Input Database Coverage: 40052468 bp out of 2296372838 bp ( 1.74 % ) Sampling Time: 00:05:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:07 (hh:mm:ss) Elapsed Time, 35827 HSPs Collected Number of families returned by RECON: 2029 Round Time: 00:36:25 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117359 repeats masked totaling 32328948 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90001759 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 90001759 bp After Masking: 57146133 bp Masked: 36.51 % -- Input Database Coverage: 130054227 bp out of 2296372838 bp ( 5.66 % ) Sampling Time: 00:16:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:16:29 (hh:mm:ss) Elapsed Time, 179474 HSPs Collected Number of families returned by RECON: 7143 Round Time: 03:40:22 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383508 repeats masked totaling 103811161 bp(s). - TE Masking time 00:06:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004826 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 270004126 bp After Masking: 164458788 bp Masked: 39.09 % -- Input Database Coverage: 400059053 bp out of 2296372838 bp ( 17.42 % ) Sampling Time: 00:52:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 24:57:26 (hh:mm:ss) Elapsed Time, 1441292 HSPs Collected Number of families returned by RECON: 30309 Round Time: 26:49:55 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatScout/RECON discovery complete: 845 families found Classification Time: 00:36:41 (hh:mm:ss) Elapsed Time Program Time: 32:26:45 (hh:mm:ss) Elapsed Time