RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2ioSdQ/RM_1346912.WedDec181113212024 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: 1734549200 Database = /dev/shm/rModeler.2ioSdQ/GCA_040894015.1_aEngPut4.paternal - Sequences = 819 - Bases = 2081032022 - N50 = 236531669 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 283748950-304016097 | [ 1 ] 263481804-283748950 | [ 1 ] 243214658-263481804 | [ ] 222947512-243214658 | [ 1 ] 202680366-222947512 | [ 1 ] 182413220-202680366 | [ 2 ] 162146074-182413220 | [ 1 ] 141878928-162146074 | [ ] 121611782-141878928 | [ 1 ] 101344636-121611782 | [ 1 ] 81077490-101344636 | [ 2 ] 60810344-81077490 | [ ] 40543198-60810344 | [ ] 20276052-40543198 | [ ] 8906-20276052 |************************************************** [ 808 ] Storage Throughput = fair ( 377.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039900 bp ( 40038300 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:07:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:29:36 (hh:mm:ss) Elapsed Time Round Time: 01:03:37 (hh:mm:ss) Elapsed Time : 673 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15372 repeats masked totaling 3641098 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032014 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10031814 bp After Masking: 4736305 bp Masked: 52.79 % -- Input Database Coverage: 10032014 bp out of 2081032022 bp ( 0.48 % ) Sampling Time: 00:09:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:06 (hh:mm:ss) Elapsed Time, 13475 HSPs Collected Number of families returned by RECON: 1355 Round Time: 00:20:49 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:19:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46884 repeats masked totaling 11025172 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007806 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30006406 bp After Masking: 13732233 bp Masked: 54.24 % -- Input Database Coverage: 40039820 bp out of 2081032022 bp ( 1.92 % ) Sampling Time: 00:37:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:52:16 (hh:mm:ss) Elapsed Time, 120528 HSPs Collected Number of families returned by RECON: 4051 Round Time: 01:32:49 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:19:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150234 repeats masked totaling 34503461 bp(s). - TE Masking time 00:06:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013827 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90009827 bp After Masking: 39584840 bp Masked: 56.02 % -- Input Database Coverage: 130053647 bp out of 2081032022 bp ( 6.25 % ) Sampling Time: 01:29:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 06:12:54 (hh:mm:ss) Elapsed Time, 317647 HSPs Collected Number of families returned by RECON: 11442 Round Time: 10:37:09 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:38:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:16:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 513520 repeats masked totaling 118194206 bp(s). - TE Masking time 00:30:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027957 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 270014357 bp After Masking: 104427246 bp Masked: 61.33 % -- Input Database Coverage: 400081604 bp out of 2081032022 bp ( 19.23 % ) Sampling Time: 05:26:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 46:34:05 (hh:mm:ss) Elapsed Time, 853287 HSPs Collected Number of families returned by RECON: 31247 Round Time: 54:07:23 (hh:mm:ss) Elapsed Time : 1105 families discovered. RepeatScout/RECON discovery complete: 2350 families found Classification Time: 04:22:03 (hh:mm:ss) Elapsed Time Program Time: 72:03:50 (hh:mm:ss) Elapsed Time