RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dq3v2k/RM_3510501.TueApr150819352025 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: 1744730374 Database = /dev/shm/rModeler.dq3v2k/GCA_043727835.1_ASM4372783v1 - Sequences = 75 - Bases = 2268696503 Storage Throughput = excellent ( 1689.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016069 bp ( 40015569 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:31 (hh:mm:ss) Elapsed Time Round Time: 00:13:48 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11596 repeats masked totaling 2593687 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000935 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000935 bp After Masking: 7284202 bp Masked: 27.16 % -- Input Database Coverage: 10000935 bp out of 2268696503 bp ( 0.44 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 5341 HSPs Collected Number of families returned by RECON: 888 Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37608 repeats masked totaling 8346686 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015054 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30014554 bp After Masking: 21191055 bp Masked: 29.40 % -- Input Database Coverage: 40015989 bp out of 2268696503 bp ( 1.76 % ) Sampling Time: 00:02:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:17 (hh:mm:ss) Elapsed Time, 87994 HSPs Collected Number of families returned by RECON: 2480 Round Time: 00:27:36 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121323 repeats masked totaling 27247041 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023238 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90022498 bp After Masking: 61529212 bp Masked: 31.65 % -- Input Database Coverage: 130039227 bp out of 2268696503 bp ( 5.73 % ) Sampling Time: 00:06:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:10:14 (hh:mm:ss) Elapsed Time, 81370 HSPs Collected Number of families returned by RECON: 9076 Round Time: 01:18:10 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 407410 repeats masked totaling 88769263 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021059 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 270017359 bp After Masking: 177493459 bp Masked: 34.27 % -- Input Database Coverage: 400060286 bp out of 2268696503 bp ( 17.63 % ) Sampling Time: 00:19:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 08:16:29 (hh:mm:ss) Elapsed Time, 236661 HSPs Collected Number of families returned by RECON: 39006 Round Time: 08:47:10 (hh:mm:ss) Elapsed Time : 404 families discovered. RepeatScout/RECON discovery complete: 877 families found Classification Time: 00:21:58 (hh:mm:ss) Elapsed Time Program Time: 11:12:29 (hh:mm:ss) Elapsed Time