RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SWHPeV/RM_2162617.MonJul221951052024 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: 1721703058 Database = /dev/shm/rModeler.SWHPeV/GCF_022539595.1_ASM2253959v1 - Sequences = 354 - Bases = 863484803 - N50 = 37359734 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41012380-43941765 | [ 3 ] 38082996-41012380 | [ 4 ] 35153612-38082996 |* [ 8 ] 32224227-35153611 | [ 5 ] 29294843-32224227 | [ ] 26365459-29294843 | [ 3 ] 23436075-26365459 | [ ] 20506690-23436074 | [ 1 ] 17577306-20506690 | [ ] 14647922-17577306 | [ ] 11718538-14647922 | [ ] 8789153-11718537 | [ ] 5859769-8789153 | [ ] 2930385-5859769 | [ ] 1001-2930385 |************************************************** [ 330 ] Storage Throughput = fair ( 666.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007037 bp ( 40000686 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:09 (hh:mm:ss) Elapsed Time Round Time: 00:32:09 (hh:mm:ss) Elapsed Time : 468 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 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9310 repeats masked totaling 1730945 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023969 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10022084 bp After Masking: 7855729 bp Masked: 21.62 % -- Input Database Coverage: 10023969 bp out of 863484803 bp ( 1.16 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:42:15 (hh:mm:ss) Elapsed Time, 10146 HSPs Collected Number of families returned by RECON: 1526 Round Time: 00:45:34 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30393 repeats masked totaling 6037832 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023136 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30018670 bp After Masking: 22675374 bp Masked: 24.46 % -- Input Database Coverage: 40047105 bp out of 863484803 bp ( 4.64 % ) Sampling Time: 00:03:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 02:28:12 (hh:mm:ss) Elapsed Time, 60869 HSPs Collected Number of families returned by RECON: 4797 Round Time: 02:38:46 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104740 repeats masked totaling 21437296 bp(s). - TE Masking time 00:01:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020332 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90006403 bp After Masking: 64987734 bp Masked: 27.80 % -- Input Database Coverage: 130067437 bp out of 863484803 bp ( 15.06 % ) Sampling Time: 00:10:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 11:07:15 (hh:mm:ss) Elapsed Time, 223174 HSPs Collected Number of families returned by RECON: 15156 Round Time: 11:50:50 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 374666 repeats masked totaling 77450777 bp(s). - TE Masking time 00:11:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270061439 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 270018842 bp After Masking: 181343214 bp Masked: 32.84 % -- Input Database Coverage: 400128876 bp out of 863484803 bp ( 46.34 % ) Sampling Time: 00:44:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 51:45:59 (hh:mm:ss) Elapsed Time, 660359 HSPs Collected Number of families returned by RECON: 54479 Round Time: 54:46:28 (hh:mm:ss) Elapsed Time : 959 families discovered. RepeatScout/RECON discovery complete: 1993 families found Classification Time: 01:16:28 (hh:mm:ss) Elapsed Time Program Time: 71:50:15 (hh:mm:ss) Elapsed Time