RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.R8Ywf4/RM_725499.FriNov151959322024 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: 1731729571 Database = /scratch/tmp/rModeler.R8Ywf4/GCA_040954625.1_ASM4095462v1 - Sequences = 77 - Bases = 328607491 Storage Throughput = excellent ( 1524.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021470 bp ( 40005970 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:46 (hh:mm:ss) Elapsed Time Round Time: 00:11:49 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7010 repeats masked totaling 1946103 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10044143 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10038643 bp After Masking: 6949194 bp Masked: 30.78 % -- Input Database Coverage: 10044143 bp out of 328607491 bp ( 3.06 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 4237 HSPs Collected Number of families returned by RECON: 790 Round Time: 00:03:36 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (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... 19006 repeats masked totaling 5823037 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017247 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30007247 bp After Masking: 21294522 bp Masked: 29.04 % -- Input Database Coverage: 40061390 bp out of 328607491 bp ( 12.19 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:09 (hh:mm:ss) Elapsed Time, 29231 HSPs Collected Number of families returned by RECON: 2736 Round Time: 00:13:33 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61379 repeats masked totaling 16574073 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90072038 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 90039538 bp After Masking: 64258184 bp Masked: 28.63 % -- Input Database Coverage: 130133428 bp out of 328607491 bp ( 39.60 % ) Sampling Time: 00:06:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 01:03:12 (hh:mm:ss) Elapsed Time, 323739 HSPs Collected Number of families returned by RECON: 10725 Round Time: 01:15:15 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156861 repeats masked totaling 44656926 bp(s). - TE Masking time 00:03:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 198473749 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 198394749 bp After Masking: 133189036 bp Masked: 32.87 % -- Input Database Coverage: 328607177 bp out of 328607491 bp ( 100.00 % ) Sampling Time: 00:15:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 12397710 Comparison Time: 04:00:33 (hh:mm:ss) Elapsed Time, 793391 HSPs Collected Number of families returned by RECON: 26055 Round Time: 04:26:29 (hh:mm:ss) Elapsed Time : 530 families discovered. RepeatScout/RECON discovery complete: 1273 families found Classification Time: 00:54:44 (hh:mm:ss) Elapsed Time Program Time: 07:05:26 (hh:mm:ss) Elapsed Time