RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ozMOlf/RM_2740218.FriJul191131142024 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: 1721413869 Database = /dev/shm/rModeler.ozMOlf/GCF_023724105.1_carGib1.2-hapl.c - Sequences = 51 - Bases = 1583351535 Storage Throughput = good ( 784.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40072685 bp ( 40033401 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:49 (hh:mm:ss) Elapsed Time Round Time: 00:31:39 (hh:mm:ss) Elapsed Time : 703 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11476 repeats masked totaling 2786371 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041437 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10033937 bp After Masking: 6690461 bp Masked: 33.32 % -- Input Database Coverage: 10041437 bp out of 1583351535 bp ( 0.63 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:23:04 (hh:mm:ss) Elapsed Time, 25889 HSPs Collected Number of families returned by RECON: 1462 Round Time: 00:25:23 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34001 repeats masked totaling 7774532 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30071248 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30039464 bp After Masking: 20334494 bp Masked: 32.31 % -- Input Database Coverage: 40112685 bp out of 1583351535 bp ( 2.53 % ) Sampling Time: 00:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 01:23:43 (hh:mm:ss) Elapsed Time, 53724 HSPs Collected Number of families returned by RECON: 5282 Round Time: 01:31:45 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113092 repeats masked totaling 25009433 bp(s). - TE Masking time 00:02:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90097371 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90026497 bp After Masking: 60353494 bp Masked: 32.96 % -- Input Database Coverage: 130210056 bp out of 1583351535 bp ( 8.22 % ) Sampling Time: 00:10:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 06:33:39 (hh:mm:ss) Elapsed Time, 387277 HSPs Collected Number of families returned by RECON: 17448 Round Time: 07:05:59 (hh:mm:ss) Elapsed Time : 633 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 410560 repeats masked totaling 94090235 bp(s). - TE Masking time 00:15:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270269367 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 270039704 bp After Masking: 162761170 bp Masked: 39.73 % -- Input Database Coverage: 400479423 bp out of 1583351535 bp ( 25.29 % ) Sampling Time: 00:37:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 26:31:17 (hh:mm:ss) Elapsed Time, 1061011 HSPs Collected Number of families returned by RECON: 56924 Round Time: 28:32:11 (hh:mm:ss) Elapsed Time : 1326 families discovered. RepeatScout/RECON discovery complete: 2784 families found Classification Time: 02:21:26 (hh:mm:ss) Elapsed Time Program Time: 40:28:23 (hh:mm:ss) Elapsed Time