RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Iao1cc/RM_5821.WedJan101935542024 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: 1704944153 Database = /dev/shm/rModeler.Iao1cc/GCA_020826835.1_mDicBic1.pat.decon - Sequences = 1199 - Bases = 3044793931 - N50 = 60201184 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 131036211-140395700 | [ 1 ] 121676723-131036211 | [ ] 112317234-121676722 | [ ] 102957746-112317234 | [ ] 93598257-102957745 | [ 3 ] 84238769-93598257 | [ 3 ] 74879280-84238768 | [ 3 ] 65519792-74879280 | [ 4 ] 56160303-65519791 | [ 6 ] 46800815-56160303 | [ 6 ] 37441326-46800814 | [ 5 ] 28081838-37441326 | [ 8 ] 18722349-28081837 | [ 8 ] 9362861-18722349 | [ 7 ] 3373-9362861 |************************************************** [ 1145 ] Storage Throughput = excellent ( 1045.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006292 bp ( 40006279 non ambiguous ) - Num Contigs Represented = 160 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:52 (hh:mm:ss) Elapsed Time Round Time: 00:36:30 (hh:mm:ss) Elapsed Time : 265 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11859 repeats masked totaling 3409130 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032247 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 10032234 bp After Masking: 6328033 bp Masked: 36.92 % -- Input Database Coverage: 10032247 bp out of 3044793931 bp ( 0.33 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 13701 HSPs Collected Number of families returned by RECON: 685 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35000 repeats masked totaling 10994152 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013969 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 30013969 bp After Masking: 17361578 bp Masked: 42.16 % -- Input Database Coverage: 40046216 bp out of 3044793931 bp ( 1.32 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:25 (hh:mm:ss) Elapsed Time, 23231 HSPs Collected Number of families returned by RECON: 1894 Round Time: 00:29:27 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111972 repeats masked totaling 32806951 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050285 bp Num Contigs Represented = 279 Non ambiguous bp: Initial: 90018345 bp After Masking: 52043130 bp Masked: 42.19 % -- Input Database Coverage: 130096501 bp out of 3044793931 bp ( 4.27 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 02:43:17 (hh:mm:ss) Elapsed Time, 92537 HSPs Collected Number of families returned by RECON: 7385 Round Time: 02:57:46 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 376790 repeats masked totaling 110174093 bp(s). - TE Masking time 00:12:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270128575 bp Num Contigs Represented = 451 Non ambiguous bp: Initial: 270038772 bp After Masking: 145474206 bp Masked: 46.13 % -- Input Database Coverage: 400225076 bp out of 3044793931 bp ( 13.14 % ) Sampling Time: 00:33:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 20:30:56 (hh:mm:ss) Elapsed Time, 291611 HSPs Collected Number of families returned by RECON: 28672 Round Time: 21:29:05 (hh:mm:ss) Elapsed Time : 353 families discovered. RepeatScout/RECON discovery complete: 881 families found Classification Time: 01:05:51 (hh:mm:ss) Elapsed Time Program Time: 26:46:23 (hh:mm:ss) Elapsed Time