RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.T6ZStp/RM_124156.SunApr130713542025
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: 1744553633
Database = /data/tmp/rModeler.T6ZStp/GCA_045843805.1_mUroPar1.hap1 - Sequences = 2530
- Bases = 2935792869
- N50 = 199381243
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
265310653-284260672 | [ 1 ]
246360635-265310653 | [ ]
227410617-246360635 | [ ]
208460598-227410616 | [ 4 ]
189510580-208460598 | [ 1 ]
170560562-189510580 | [ 1 ]
151610543-170560561 | [ 1 ]
132660525-151610543 | [ 2 ]
113710507-132660525 | [ 2 ]
94760488-113710506 | [ 1 ]
75810470-94760488 | [ ]
56860452-75810470 | [ 4 ]
37910433-56860451 | [ ]
18960415-37910433 | [ 1 ]
10397-18960415 |************************************************** [ 2512 ]
Storage Throughput = excellent ( 1066.91 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40038069 bp ( 40036369 non ambiguous )
- Num Contigs Represented = 112
- Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:16:19 (hh:mm:ss) Elapsed Time
Round Time: 00:27:06 (hh:mm:ss) Elapsed Time : 216 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
9519 repeats masked totaling 1972692 bp(s).
- TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10036065 bp
Num Contigs Represented = 46
Non ambiguous bp:
Initial: 10035665 bp
After Masking: 7519256 bp
Masked: 25.07 %
-- Input Database Coverage: 10036065 bp out of 2935792869 bp ( 0.34 % )
Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 32640
Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 6470 HSPs Collected
Number of families returned by RECON: 764
Round Time: 00:09:05 (hh:mm:ss) Elapsed Time : 18 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
32860 repeats masked totaling 6660094 bp(s).
- TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30001924 bp
Num Contigs Represented = 90
Non ambiguous bp:
Initial: 30000624 bp
After Masking: 21925442 bp
Masked: 26.92 %
-- Input Database Coverage: 40037989 bp out of 2935792869 bp ( 1.36 % )
Sampling Time: 00:05:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 287661
Comparison Time: 00:34:58 (hh:mm:ss) Elapsed Time, 44431 HSPs Collected
Number of families returned by RECON: 2352
Round Time: 01:23:45 (hh:mm:ss) Elapsed Time : 54 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:07:07 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:06:15 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
106851 repeats masked totaling 23979142 bp(s).
- TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90040110 bp
Num Contigs Represented = 209
Non ambiguous bp:
Initial: 90037010 bp
After Masking: 62066268 bp
Masked: 31.07 %
-- Input Database Coverage: 130078099 bp out of 2935792869 bp ( 4.43 % )
Sampling Time: 00:14:55 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2616328
Comparison Time: 02:59:50 (hh:mm:ss) Elapsed Time, 185580 HSPs Collected
Number of families returned by RECON: 8808
Round Time: 03:26:26 (hh:mm:ss) Elapsed Time : 167 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:22:07 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:20:47 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
361414 repeats masked totaling 78248524 bp(s).
- TE Masking time 00:05:50 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270019524 bp
Num Contigs Represented = 515
Non ambiguous bp:
Initial: 270009624 bp
After Masking: 177631168 bp
Masked: 34.21 %
-- Input Database Coverage: 400097623 bp out of 2935792869 bp ( 13.63 % )
Sampling Time: 00:49:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23567545
Comparison Time: 22:55:00 (hh:mm:ss) Elapsed Time, 1519702 HSPs Collected
Number of families returned by RECON: 36066
Round Time: 25:19:29 (hh:mm:ss) Elapsed Time : 410 families discovered.
RepeatScout/RECON discovery complete: 865 families found
Classification Time: 01:04:41 (hh:mm:ss) Elapsed Time
Program Time: 31:50:32 (hh:mm:ss) Elapsed Time