RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Y8bRka/RM_1433340.ThuJul110627282024 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: 1720704448 Database = /dev/shm/rModeler.Y8bRka/GCF_029220125.1_NWPU_hadal_v1 - Sequences = 200 - Bases = 626455521 - N50 = 25961070 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32814470-35158290 | [ 1 ] 30470651-32814470 | [ 2 ] 28126831-30470650 |* [ 6 ] 25783012-28126831 | [ 1 ] 23439193-25783012 |** [ 8 ] 21095373-23439192 | [ 3 ] 18751554-21095373 | [ 2 ] 16407734-18751553 | [ ] 14063915-16407734 | [ ] 11720096-14063915 | [ 1 ] 9376276-11720095 | [ ] 7032457-9376276 | [ ] 4688637-7032456 | [ ] 2344818-4688637 | [ 1 ] 999-2344818 |************************************************** [ 175 ] Storage Throughput = excellent ( 1043.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40087900 bp ( 40027101 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:05 (hh:mm:ss) Elapsed Time Round Time: 00:24:37 (hh:mm:ss) Elapsed Time : 449 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6379 repeats masked totaling 1837047 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042933 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10026781 bp After Masking: 6972632 bp Masked: 30.46 % -- Input Database Coverage: 10042933 bp out of 626455521 bp ( 1.60 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:09:35 (hh:mm:ss) Elapsed Time, 12376 HSPs Collected Number of families returned by RECON: 1039 Round Time: 00:13:42 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21214 repeats masked totaling 5897257 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044948 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30000301 bp After Masking: 21103746 bp Masked: 29.65 % -- Input Database Coverage: 40087881 bp out of 626455521 bp ( 6.40 % ) Sampling Time: 00:08:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:30:58 (hh:mm:ss) Elapsed Time, 33411 HSPs Collected Number of families returned by RECON: 3954 Round Time: 00:40:04 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69253 repeats masked totaling 18792025 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90115756 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90021475 bp After Masking: 62144523 bp Masked: 30.97 % -- Input Database Coverage: 130203637 bp out of 626455521 bp ( 20.78 % ) Sampling Time: 00:23:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:53:31 (hh:mm:ss) Elapsed Time, 197637 HSPs Collected Number of families returned by RECON: 15448 Round Time: 04:23:32 (hh:mm:ss) Elapsed Time : 324 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:06:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 251992 repeats masked totaling 65895960 bp(s). - TE Masking time 00:07:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270418628 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 270006282 bp After Masking: 175140919 bp Masked: 35.13 % -- Input Database Coverage: 400622265 bp out of 626455521 bp ( 63.95 % ) Sampling Time: 01:17:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 19:45:06 (hh:mm:ss) Elapsed Time, 663004 HSPs Collected Number of families returned by RECON: 58524 Round Time: 22:13:04 (hh:mm:ss) Elapsed Time : 825 families discovered. RepeatScout/RECON discovery complete: 1659 families found Classification Time: 01:30:54 (hh:mm:ss) Elapsed Time Program Time: 29:25:53 (hh:mm:ss) Elapsed Time