RepeatModeler Version 2.0.4
===========================
Using output directory = /scratch/tmp/rModeler.lZlCuG/RM_3587060.FriDec60330192024
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: 1733484619
Database = /scratch/tmp/rModeler.lZlCuG/GCA_964196065.1_bCalBor7.hap2.1 - Sequences = 249
- Bases = 1169960687
- N50 = 129082959
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
206221202-220951217 | [ 1 ]
191491188-206221202 | [ ]
176761173-191491187 | [ ]
162031159-176761173 | [ 1 ]
147301144-162031158 | [ ]
132571130-147301144 | [ ]
117841115-132571129 | [ 1 ]
103111101-117841115 | [ ]
88381086-103111100 | [ ]
73651072-88381086 | [ 1 ]
58921057-73651071 | [ ]
44191043-58921057 | [ 3 ]
29461028-44191042 | [ 2 ]
14731014-29461028 |** [ 11 ]
1000-14731014 |************************************************** [ 229 ]
Storage Throughput = excellent ( 1551.00 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40030613 bp ( 40027813 non ambiguous )
- Num Contigs Represented = 53
- Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:07:56 (hh:mm:ss) Elapsed Time
Round Time: 00:16:45 (hh:mm:ss) Elapsed Time : 54 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
1157 repeats masked totaling 558998 bp(s).
- TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10001310 bp
Num Contigs Represented = 31
Non ambiguous bp:
Initial: 10001110 bp
After Masking: 9255645 bp
Masked: 7.45 %
-- Input Database Coverage: 10001310 bp out of 1169960687 bp ( 0.85 % )
Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31125
Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 872 HSPs Collected
Number of families returned by RECON: 266
Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 4 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:49 (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...
4258 repeats masked totaling 2007629 bp(s).
- TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30029223 bp
Num Contigs Represented = 50
Non ambiguous bp:
Initial: 30026623 bp
After Masking: 27224258 bp
Masked: 9.33 %
-- Input Database Coverage: 40030533 bp out of 1169960687 bp ( 3.42 % )
Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 283881
Comparison Time: 00:13:57 (hh:mm:ss) Elapsed Time, 11497 HSPs Collected
Number of families returned by RECON: 1337
Round Time: 00:16:15 (hh:mm:ss) Elapsed Time : 11 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
14666 repeats masked totaling 6353797 bp(s).
- TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90010762 bp
Num Contigs Represented = 77
Non ambiguous bp:
Initial: 90002562 bp
After Masking: 81271412 bp
Masked: 9.70 %
-- Input Database Coverage: 130041295 bp out of 1169960687 bp ( 11.12 % )
Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2548153
Comparison Time: 01:30:22 (hh:mm:ss) Elapsed Time, 57357 HSPs Collected
Number of families returned by RECON: 7734
Round Time: 01:37:17 (hh:mm:ss) Elapsed Time : 66 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:06:53 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
53139 repeats masked totaling 21020448 bp(s).
- TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270033975 bp
Num Contigs Represented = 143
Non ambiguous bp:
Initial: 270011375 bp
After Masking: 242334652 bp
Masked: 10.25 %
-- Input Database Coverage: 400075270 bp out of 1169960687 bp ( 34.20 % )
Sampling Time: 00:18:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 22960476
Comparison Time: 11:41:34 (hh:mm:ss) Elapsed Time, 177793 HSPs Collected
Number of families returned by RECON: 52107
Round Time: 12:17:15 (hh:mm:ss) Elapsed Time : 229 families discovered.
RepeatScout/RECON discovery complete: 364 families found
Classification Time: 00:10:24 (hh:mm:ss) Elapsed Time
Program Time: 14:41:35 (hh:mm:ss) Elapsed Time