RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.inPTJv/RM_1643739.TueMar41041242025 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: 1741113683 Database = /dev/shm/rModeler.inPTJv/GCA_048126635.1_SpiSpi1_v1.hap1 - Sequences = 38 - Bases = 407561107 Storage Throughput = excellent ( 1747.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029559 bp ( 40026859 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:19 (hh:mm:ss) Elapsed Time Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1640 repeats masked totaling 303114 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031816 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10031016 bp After Masking: 9064492 bp Masked: 9.64 % -- Input Database Coverage: 10031816 bp out of 407561107 bp ( 2.46 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 4525 HSPs Collected Number of families returned by RECON: 740 Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5965 repeats masked totaling 1004157 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037748 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30035848 bp After Masking: 26816031 bp Masked: 10.72 % -- Input Database Coverage: 40069564 bp out of 407561107 bp ( 9.83 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:42 (hh:mm:ss) Elapsed Time, 20511 HSPs Collected Number of families returned by RECON: 3721 Round Time: 00:14:54 (hh:mm:ss) Elapsed Time : 41 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20999 repeats masked totaling 3479687 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030532 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90024732 bp After Masking: 79888548 bp Masked: 11.26 % -- Input Database Coverage: 130100096 bp out of 407561107 bp ( 31.92 % ) Sampling Time: 00:06:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:18:41 (hh:mm:ss) Elapsed Time, 210816 HSPs Collected Number of families returned by RECON: 16725 Round Time: 01:27:59 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86814 repeats masked totaling 14972257 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040335 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 270025335 bp After Masking: 235861156 bp Masked: 12.65 % -- Input Database Coverage: 400140431 bp out of 407561107 bp ( 98.18 % ) Sampling Time: 00:18:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 09:52:12 (hh:mm:ss) Elapsed Time, 1346573 HSPs Collected Number of families returned by RECON: 73986 Round Time: 10:49:02 (hh:mm:ss) Elapsed Time : 579 families discovered. RepeatScout/RECON discovery complete: 977 families found Classification Time: 00:20:11 (hh:mm:ss) Elapsed Time Program Time: 13:05:04 (hh:mm:ss) Elapsed Time