RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ez7DnS/RM_29193.WedDec282307322022 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: 1672297651 Database = /dev/shm/rModeler.ez7DnS/GCF_013358815.1_fEleEle1.pri - Sequences = 89 - Bases = 589358956 Storage Throughput = excellent ( 1073.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41087263 bp ( 40005470 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:30:09 (hh:mm:ss) Elapsed Time Round Time: 00:35:11 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4124 repeats masked totaling 757036 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10295956 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10026421 bp After Masking: 8364144 bp Masked: 16.58 % -- Input Database Coverage: 10295956 bp out of 589358956 bp ( 1.75 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:06:34 (hh:mm:ss) Elapsed Time, 29754 HSPs Collected Number of families returned by RECON: 910 Round Time: 00:09:40 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11012 repeats masked totaling 2078530 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30831170 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30018912 bp After Masking: 25159128 bp Masked: 16.19 % -- Input Database Coverage: 41127126 bp out of 589358956 bp ( 6.98 % ) Sampling Time: 00:08:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299151 Comparison Time: 00:35:29 (hh:mm:ss) Elapsed Time, 28918 HSPs Collected Number of families returned by RECON: 4174 Round Time: 00:45:48 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40168 repeats masked totaling 7987125 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91699817 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90035587 bp After Masking: 73608033 bp Masked: 18.25 % -- Input Database Coverage: 132826943 bp out of 589358956 bp ( 22.54 % ) Sampling Time: 00:23:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2641551 Comparison Time: 04:03:15 (hh:mm:ss) Elapsed Time, 146816 HSPs Collected Number of families returned by RECON: 15997 Round Time: 04:35:58 (hh:mm:ss) Elapsed Time : 261 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:09:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158070 repeats masked totaling 32137757 bp(s). - TE Masking time 00:08:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274614285 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270014125 bp After Masking: 212128892 bp Masked: 21.44 % -- Input Database Coverage: 407441228 bp out of 589358956 bp ( 69.13 % ) Sampling Time: 01:22:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23650003 Comparison Time: 30:58:47 (hh:mm:ss) Elapsed Time, 647203 HSPs Collected Number of families returned by RECON: 63702 Round Time: 34:04:02 (hh:mm:ss) Elapsed Time : 804 families discovered. RepeatScout/RECON discovery complete: 1386 families found Classification Time: 01:28:21 (hh:mm:ss) Elapsed Time Program Time: 41:39:00 (hh:mm:ss) Elapsed Time