RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hpANtv/RM_1855881.TueApr220817492025 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: 1745335068 Database = /dev/shm/rModeler.hpANtv/GCA_964264875.2_mNycLei1.hap1.2 - Sequences = 585 - Bases = 2226338041 - N50 = 100879271 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215912234-231334465 | [ 1 ] 200490003-215912234 | [ 2 ] 185067772-200490003 | [ ] 169645541-185067772 | [ ] 154223310-169645541 | [ ] 138801079-154223310 | [ ] 123378848-138801079 | [ ] 107956617-123378848 | [ 2 ] 92534386-107956617 | [ 3 ] 77112155-92534386 | [ 3 ] 61689924-77112155 | [ 2 ] 46267693-61689924 | [ 5 ] 30845462-46267693 | [ 1 ] 15423231-30845462 | [ 2 ] 1000-15423231 |************************************************** [ 564 ] Storage Throughput = excellent ( 1766.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022481 bp ( 40021681 non ambiguous ) - Num Contigs Represented = 112 - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:32 (hh:mm:ss) Elapsed Time Round Time: 00:14:15 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13803 repeats masked totaling 2899406 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025158 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10025158 bp After Masking: 6024560 bp Masked: 39.91 % -- Input Database Coverage: 10025158 bp out of 2226338041 bp ( 0.45 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 68750 HSPs Collected Number of families returned by RECON: 631 Round Time: 00:04:54 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47468 repeats masked totaling 9440903 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037323 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 30036523 bp After Masking: 17704966 bp Masked: 41.06 % -- Input Database Coverage: 40062481 bp out of 2226338041 bp ( 1.80 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:11:51 (hh:mm:ss) Elapsed Time, 18045 HSPs Collected Number of families returned by RECON: 1964 Round Time: 00:16:04 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148890 repeats masked totaling 28714896 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032471 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 90029179 bp After Masking: 52893561 bp Masked: 41.25 % -- Input Database Coverage: 130094952 bp out of 2226338041 bp ( 5.84 % ) Sampling Time: 00:12:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:07:30 (hh:mm:ss) Elapsed Time, 122462 HSPs Collected Number of families returned by RECON: 6936 Round Time: 01:22:40 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 488493 repeats masked totaling 94964356 bp(s). - TE Masking time 00:04:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017031 bp Num Contigs Represented = 294 Non ambiguous bp: Initial: 270011476 bp After Masking: 149642139 bp Masked: 44.58 % -- Input Database Coverage: 400111983 bp out of 2226338041 bp ( 17.97 % ) Sampling Time: 00:39:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 07:40:43 (hh:mm:ss) Elapsed Time, 331591 HSPs Collected Number of families returned by RECON: 26648 Round Time: 08:30:29 (hh:mm:ss) Elapsed Time : 522 families discovered. RepeatScout/RECON discovery complete: 1146 families found Classification Time: 00:31:57 (hh:mm:ss) Elapsed Time Program Time: 11:00:19 (hh:mm:ss) Elapsed Time