RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.e4bCto/RM_1398193.FriMar292301382024 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: 1711778498 Database = /dev/shm/rModeler.e4bCto/GCA_963924675.1_mPhoPho1.1 - Sequences = 440 - Bases = 2512729496 - N50 = 115377316 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 174771118-187254698 | [ 2 ] 162287538-174771117 | [ 1 ] 149803958-162287537 | [ ] 137320378-149803957 | [ 2 ] 124836798-137320377 | [ 1 ] 112353218-124836797 | [ 2 ] 99869638-112353217 | [ 4 ] 87386059-99869638 | [ 4 ] 74902479-87386058 | [ 3 ] 62418899-74902478 | [ ] 49935319-62418898 | [ 2 ] 37451739-49935318 | [ ] 24968159-37451738 | [ 1 ] 12484579-24968158 | [ ] 1000-12484579 |************************************************** [ 418 ] Storage Throughput = good ( 986.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006112 bp ( 40003912 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:24 (hh:mm:ss) Elapsed Time Round Time: 00:31:15 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9505 repeats masked totaling 2841720 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009194 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10008194 bp After Masking: 7031384 bp Masked: 29.74 % -- Input Database Coverage: 10009194 bp out of 2512729496 bp ( 0.40 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 45748 HSPs Collected Number of families returned by RECON: 895 Round Time: 00:09:08 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32838 repeats masked totaling 10114640 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036916 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30035716 bp After Masking: 19614445 bp Masked: 34.70 % -- Input Database Coverage: 40046110 bp out of 2512729496 bp ( 1.59 % ) Sampling Time: 00:03:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:10:45 (hh:mm:ss) Elapsed Time, 36335 HSPs Collected Number of families returned by RECON: 2245 Round Time: 01:16:21 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105086 repeats masked totaling 32539103 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017423 bp Num Contigs Represented = 123 Non ambiguous bp: Initial: 90010823 bp After Masking: 56202924 bp Masked: 37.56 % -- Input Database Coverage: 130063533 bp out of 2512729496 bp ( 5.18 % ) Sampling Time: 00:10:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:03:26 (hh:mm:ss) Elapsed Time, 339594 HSPs Collected Number of families returned by RECON: 8129 Round Time: 03:16:56 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 356910 repeats masked totaling 103551960 bp(s). - TE Masking time 00:04:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270058842 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 270038042 bp After Masking: 162053910 bp Masked: 39.99 % -- Input Database Coverage: 400122375 bp out of 2512729496 bp ( 15.92 % ) Sampling Time: 00:34:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 20:05:58 (hh:mm:ss) Elapsed Time, 1154204 HSPs Collected Number of families returned by RECON: 33761 Round Time: 21:01:40 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatScout/RECON discovery complete: 787 families found Classification Time: 00:26:44 (hh:mm:ss) Elapsed Time Program Time: 26:42:04 (hh:mm:ss) Elapsed Time