RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ge4j5t/RM_1436707.FriNov151916292024 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: 1731726988 Database = /scratch/tmp/rModeler.ge4j5t/GCF_963924675.1_mPhoPho1.1 - Sequences = 439 - Bases = 2512713112 - 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 |************************************************** [ 417 ] Storage Throughput = excellent ( 1501.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009888 bp ( 40007888 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:13 (hh:mm:ss) Elapsed Time Round Time: 00:16:03 (hh:mm:ss) Elapsed Time : 199 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9399 repeats masked totaling 2753585 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039413 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10039213 bp After Masking: 7134031 bp Masked: 28.94 % -- Input Database Coverage: 10039413 bp out of 2512713112 bp ( 0.40 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 83197 HSPs Collected Number of families returned by RECON: 904 Round Time: 00:04:46 (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 : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32987 repeats masked totaling 9819738 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010395 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30008595 bp After Masking: 19680408 bp Masked: 34.42 % -- Input Database Coverage: 40049808 bp out of 2512713112 bp ( 1.59 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:13:43 (hh:mm:ss) Elapsed Time, 46828 HSPs Collected Number of families returned by RECON: 2485 Round Time: 00:16:22 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111279 repeats masked totaling 31633232 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043211 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 90037411 bp After Masking: 57061012 bp Masked: 36.63 % -- Input Database Coverage: 130093019 bp out of 2512713112 bp ( 5.18 % ) Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:23:48 (hh:mm:ss) Elapsed Time, 204736 HSPs Collected Number of families returned by RECON: 8784 Round Time: 01:31:24 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 373393 repeats masked totaling 104618683 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036505 bp Num Contigs Represented = 217 Non ambiguous bp: Initial: 270016211 bp After Masking: 161094201 bp Masked: 40.34 % -- Input Database Coverage: 400129524 bp out of 2512713112 bp ( 15.92 % ) Sampling Time: 00:18:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 08:17:20 (hh:mm:ss) Elapsed Time, 1744749 HSPs Collected Number of families returned by RECON: 31406 Round Time: 08:44:38 (hh:mm:ss) Elapsed Time : 310 families discovered. RepeatScout/RECON discovery complete: 776 families found Classification Time: 00:14:00 (hh:mm:ss) Elapsed Time Program Time: 11:07:13 (hh:mm:ss) Elapsed Time