RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FXcf8h/RM_3071085.ThuJun271226052024 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: 1719516365 Database = /dev/shm/rModeler.FXcf8h/GCF_036172605.1_aPelFus1.pri - Sequences = 159 - Bases = 3606456729 - N50 = 427915699 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 466172540-499470508 | [ 1 ] 432874573-466172540 | [ 1 ] 399576606-432874573 | [ 1 ] 366278639-399576606 | [ 2 ] 332980672-366278639 | [ ] 299682704-332980671 | [ 1 ] 266384737-299682704 | [ ] 233086770-266384737 | [ ] 199788803-233086770 | [ 1 ] 166490836-199788803 | [ 2 ] 133192868-166490835 |* [ 3 ] 99894901-133192868 | [ 1 ] 66596934-99894901 | [ ] 33298967-66596934 | [ ] 1000-33298967 |************************************************** [ 146 ] Storage Throughput = excellent ( 1367.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010398 bp ( 40009998 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:06:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:06 (hh:mm:ss) Elapsed Time Round Time: 00:40:56 (hh:mm:ss) Elapsed Time : 777 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14850 repeats masked totaling 4358172 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007585 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10007585 bp After Masking: 4554831 bp Masked: 54.49 % -- Input Database Coverage: 10007585 bp out of 3606456729 bp ( 0.28 % ) Sampling Time: 00:07:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:19 (hh:mm:ss) Elapsed Time, 15617 HSPs Collected Number of families returned by RECON: 1214 Round Time: 00:12:28 (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 : 00:06:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47505 repeats masked totaling 13567024 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002812 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30002412 bp After Masking: 13439526 bp Masked: 55.21 % -- Input Database Coverage: 40010397 bp out of 3606456729 bp ( 1.11 % ) Sampling Time: 00:17:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:20:26 (hh:mm:ss) Elapsed Time, 50718 HSPs Collected Number of families returned by RECON: 4103 Round Time: 00:38:45 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:15:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149479 repeats masked totaling 41942894 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039206 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90037406 bp After Masking: 38932869 bp Masked: 56.76 % -- Input Database Coverage: 130049603 bp out of 3606456729 bp ( 3.61 % ) Sampling Time: 00:40:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:04:22 (hh:mm:ss) Elapsed Time, 277240 HSPs Collected Number of families returned by RECON: 12002 Round Time: 02:52:36 (hh:mm:ss) Elapsed Time : 412 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:44:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 502142 repeats masked totaling 138803854 bp(s). - TE Masking time 00:11:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019611 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270015185 bp After Masking: 104348611 bp Masked: 61.35 % -- Input Database Coverage: 400069214 bp out of 3606456729 bp ( 11.09 % ) Sampling Time: 02:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 14:23:22 (hh:mm:ss) Elapsed Time, 938488 HSPs Collected Number of families returned by RECON: 32160 Round Time: 17:09:56 (hh:mm:ss) Elapsed Time : 1169 families discovered. RepeatScout/RECON discovery complete: 2454 families found Classification Time: 01:40:11 (hh:mm:ss) Elapsed Time Program Time: 23:14:52 (hh:mm:ss) Elapsed Time