RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.g5IR4Z/RM_11589.FriJan120854192024 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: 1705078455 Database = /dev/shm/rModeler.g5IR4Z/GCA_030704935.1_ASM3070493v1 - Sequences = 379 - Bases = 2671498991 - N50 = 146333500 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 271115113-290480407 | [ 1 ] 251749819-271115112 | [ ] 232384525-251749818 | [ ] 213019231-232384524 | [ 1 ] 193653938-213019231 | [ ] 174288644-193653937 | [ 1 ] 154923350-174288643 | [ 2 ] 135558056-154923349 | [ 6 ] 116192762-135558055 | [ 1 ] 96827469-116192762 | [ 1 ] 77462175-96827468 | [ 3 ] 58096881-77462174 | [ 3 ] 38731587-58096880 | [ ] 19366293-38731586 | [ 1 ] 1000-19366293 |************************************************** [ 359 ] Storage Throughput = excellent ( 1157.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040728 bp ( 40036228 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:41 (hh:mm:ss) Elapsed Time Round Time: 00:32:14 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12050 repeats masked totaling 2520595 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005472 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10005472 bp After Masking: 6889171 bp Masked: 31.15 % -- Input Database Coverage: 10005472 bp out of 2671498991 bp ( 0.37 % ) Sampling Time: 00:02:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:15:11 (hh:mm:ss) Elapsed Time, 172822 HSPs Collected Number of families returned by RECON: 737 Round Time: 00:47:51 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41619 repeats masked totaling 9010749 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035176 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30030676 bp After Masking: 19679654 bp Masked: 34.47 % -- Input Database Coverage: 40040648 bp out of 2671498991 bp ( 1.50 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:36:36 (hh:mm:ss) Elapsed Time, 660110 HSPs Collected Number of families returned by RECON: 2065 Round Time: 00:44:20 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131797 repeats masked totaling 29110582 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042415 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90031415 bp After Masking: 56101428 bp Masked: 37.69 % -- Input Database Coverage: 130083063 bp out of 2671498991 bp ( 4.87 % ) Sampling Time: 00:20:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 05:57:31 (hh:mm:ss) Elapsed Time, 5594613 HSPs Collected Number of families returned by RECON: 7432 Round Time: 06:23:45 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 440867 repeats masked totaling 92985492 bp(s). - TE Masking time 00:07:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062625 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 270020278 bp After Masking: 162438001 bp Masked: 39.84 % -- Input Database Coverage: 400145688 bp out of 2671498991 bp ( 14.98 % ) Sampling Time: 01:07:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 32:29:12 (hh:mm:ss) Elapsed Time, 44382123 HSPs Collected Number of families returned by RECON: 32121 Round Time: 35:08:43 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatScout/RECON discovery complete: 750 families found Classification Time: 00:35:46 (hh:mm:ss) Elapsed Time Program Time: 44:12:39 (hh:mm:ss) Elapsed Time