RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kGjjFM/RM_32304.ThuNov231906292023 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: 1700795187 Database = /dev/shm/rModeler.kGjjFM/GCF_028018385.1_mNeoNeb1.pri - Sequences = 33 - Bases = 2468345093 Storage Throughput = excellent ( 1178.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001403 bp ( 40000213 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:03:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:58 (hh:mm:ss) Elapsed Time Round Time: 00:31:09 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12791 repeats masked totaling 2738659 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040313 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10039813 bp After Masking: 7153706 bp Masked: 28.75 % -- Input Database Coverage: 10040313 bp out of 2468345093 bp ( 0.41 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:54 (hh:mm:ss) Elapsed Time, 5236 HSPs Collected Number of families returned by RECON: 804 Round Time: 00:09:55 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41128 repeats masked totaling 8847399 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000932 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30000242 bp After Masking: 20855234 bp Masked: 30.48 % -- Input Database Coverage: 40041245 bp out of 2468345093 bp ( 1.62 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:37:27 (hh:mm:ss) Elapsed Time, 21718 HSPs Collected Number of families returned by RECON: 2281 Round Time: 00:42:55 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131702 repeats masked totaling 28238315 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90083229 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90036181 bp After Masking: 60825220 bp Masked: 32.44 % -- Input Database Coverage: 130124474 bp out of 2468345093 bp ( 5.27 % ) Sampling Time: 00:12:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 04:29:25 (hh:mm:ss) Elapsed Time, 95706 HSPs Collected Number of families returned by RECON: 8737 Round Time: 04:47:02 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 436168 repeats masked totaling 92902422 bp(s). - TE Masking time 00:07:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270089128 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270011931 bp After Masking: 174438337 bp Masked: 35.40 % -- Input Database Coverage: 400213602 bp out of 2468345093 bp ( 16.21 % ) Sampling Time: 00:40:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 27:51:31 (hh:mm:ss) Elapsed Time, 165948 HSPs Collected Number of families returned by RECON: 35081 Round Time: 29:08:19 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatScout/RECON discovery complete: 739 families found Classification Time: 00:30:51 (hh:mm:ss) Elapsed Time Program Time: 35:50:11 (hh:mm:ss) Elapsed Time