RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PPhPng/RM_17792.WedDec61302402023 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: 1701896557 Database = /dev/shm/rModeler.PPhPng/GCA_949319135.1_fSquCep2.1 - Sequences = 106 - Bases = 1101930522 - N50 = 45672686 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 66026216-70742303 | [ 1 ] 61310129-66026215 |* [ 2 ] 56594042-61310128 | [ ] 51877955-56594041 | [ 1 ] 47161868-51877954 |** [ 4 ] 42445781-47161867 |* [ 2 ] 37729694-42445780 |*** [ 5 ] 33013608-37729694 |**** [ 7 ] 28297521-33013607 |* [ 3 ] 23581434-28297520 | [ ] 18865347-23581433 | [ ] 14149260-18865346 | [ ] 9433173-14149259 | [ ] 4717086-9433172 | [ ] 1000-4717086 |************************************************** [ 81 ] Storage Throughput = excellent ( 1123.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034794 bp ( 40031194 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:49 (hh:mm:ss) Elapsed Time Round Time: 00:35:10 (hh:mm:ss) Elapsed Time : 1195 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15159 repeats masked totaling 3312287 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026735 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10025135 bp After Masking: 6167459 bp Masked: 38.48 % -- Input Database Coverage: 10026735 bp out of 1101930522 bp ( 0.91 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:43 (hh:mm:ss) Elapsed Time, 12031 HSPs Collected Number of families returned by RECON: 1775 Round Time: 00:09:37 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48510 repeats masked totaling 10264537 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007979 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30005979 bp After Masking: 17866182 bp Masked: 40.46 % -- Input Database Coverage: 40034714 bp out of 1101930522 bp ( 3.63 % ) Sampling Time: 00:05:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:12 (hh:mm:ss) Elapsed Time, 73212 HSPs Collected Number of families returned by RECON: 6129 Round Time: 00:40:05 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157168 repeats masked totaling 32662917 bp(s). - TE Masking time 00:04:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013181 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90002307 bp After Masking: 51640803 bp Masked: 42.62 % -- Input Database Coverage: 130047895 bp out of 1101930522 bp ( 11.80 % ) Sampling Time: 00:17:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:29:29 (hh:mm:ss) Elapsed Time, 444976 HSPs Collected Number of families returned by RECON: 16993 Round Time: 04:10:44 (hh:mm:ss) Elapsed Time : 730 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 562037 repeats masked totaling 117630993 bp(s). - TE Masking time 00:22:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052408 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270021085 bp After Masking: 135517099 bp Masked: 49.81 % -- Input Database Coverage: 400100303 bp out of 1101930522 bp ( 36.31 % ) Sampling Time: 01:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 23:08:45 (hh:mm:ss) Elapsed Time, 1273853 HSPs Collected Number of families returned by RECON: 45592 Round Time: 26:06:57 (hh:mm:ss) Elapsed Time : 1845 families discovered. RepeatScout/RECON discovery complete: 3939 families found Classification Time: 02:59:17 (hh:mm:ss) Elapsed Time Program Time: 34:41:50 (hh:mm:ss) Elapsed Time