RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SIKsbu/RM_2708212.TueApr222311442025 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: 1745388704 Database = /dev/shm/rModeler.SIKsbu/GCA_964146895.2_mMinSch1.hap1.2 - Sequences = 186 - Bases = 1850590334 - N50 = 91043390 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188826873-202313579 | [ 1 ] 175340168-188826873 | [ 1 ] 161853463-175340168 | [ ] 148366757-161853462 | [ ] 134880052-148366757 | [ ] 121393347-134880052 | [ ] 107906642-121393347 | [ ] 94419936-107906641 | [ 3 ] 80933231-94419936 |* [ 6 ] 67446526-80933231 | [ 2 ] 53959821-67446526 | [ 2 ] 40473115-53959820 |* [ 4 ] 26986410-40473115 | [ 2 ] 13499705-26986410 | [ 3 ] 13000-13499705 |************************************************** [ 162 ] Storage Throughput = excellent ( 1848.32 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011035 bp ( 40010635 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:19 (hh:mm:ss) Elapsed Time Round Time: 00:11:03 (hh:mm:ss) Elapsed Time : 184 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 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8129 repeats masked totaling 1667221 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028412 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10028412 bp After Masking: 8041530 bp Masked: 19.81 % -- Input Database Coverage: 10028412 bp out of 1850590334 bp ( 0.54 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 6870 HSPs Collected Number of families returned by RECON: 944 Round Time: 00:03:53 (hh:mm:ss) Elapsed Time : 19 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 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30467 repeats masked totaling 6161523 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022543 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30022143 bp After Masking: 22611985 bp Masked: 24.68 % -- Input Database Coverage: 40050955 bp out of 1850590334 bp ( 2.16 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:13:17 (hh:mm:ss) Elapsed Time, 31386 HSPs Collected Number of families returned by RECON: 2469 Round Time: 00:16:52 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98777 repeats masked totaling 21054843 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027490 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90026890 bp After Masking: 65791177 bp Masked: 26.92 % -- Input Database Coverage: 130078445 bp out of 1850590334 bp ( 7.03 % ) Sampling Time: 00:08:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:20:41 (hh:mm:ss) Elapsed Time, 211229 HSPs Collected Number of families returned by RECON: 8502 Round Time: 01:29:59 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 326422 repeats masked totaling 68433172 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032466 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 270029015 bp After Masking: 191574389 bp Masked: 29.05 % -- Input Database Coverage: 400110911 bp out of 1850590334 bp ( 21.62 % ) Sampling Time: 00:25:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 09:21:01 (hh:mm:ss) Elapsed Time, 1491560 HSPs Collected Number of families returned by RECON: 39265 Round Time: 09:57:51 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatScout/RECON discovery complete: 796 families found Classification Time: 00:14:07 (hh:mm:ss) Elapsed Time Program Time: 12:13:45 (hh:mm:ss) Elapsed Time