RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.eCqMmn/RM_256260.SunApr201213342025
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: 1745176413
Database = /data/tmp/rModeler.eCqMmn/GCA_021292165.1_IOZ_Scro_1.0 - Sequences = 1553
- Bases = 2189995079
- N50 = 297441109
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
299808754-321223554 | [ 2 ]
278393954-299808753 | [ 2 ]
256979155-278393954 | [ ]
235564355-256979154 | [ ]
214149556-235564355 | [ 1 ]
192734756-214149555 | [ ]
171319956-192734755 | [ ]
149905157-171319956 | [ ]
128490357-149905156 | [ 1 ]
107075558-128490357 | [ ]
85660758-107075557 | [ 1 ]
64245958-85660757 | [ ]
42831159-64245958 | [ ]
21416359-42831158 | [ 8 ]
1560-21416359 |************************************************** [ 1538 ]
Storage Throughput = good ( 807.77 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40035072 bp ( 40033672 non ambiguous )
- Num Contigs Represented = 118
- Sequence extraction : 00:04:46 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:14:21 (hh:mm:ss) Elapsed Time
Round Time: 00:29:52 (hh:mm:ss) Elapsed Time : 735 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
22981 repeats masked totaling 4118064 bp(s).
- TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10024657 bp
Num Contigs Represented = 40
Non ambiguous bp:
Initial: 10024357 bp
After Masking: 5780204 bp
Masked: 42.34 %
-- Input Database Coverage: 10024657 bp out of 2189995079 bp ( 0.46 % )
Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31878
Comparison Time: 00:04:29 (hh:mm:ss) Elapsed Time, 10240 HSPs Collected
Number of families returned by RECON: 1563
Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 31 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
73297 repeats masked totaling 12785379 bp(s).
- TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30010335 bp
Num Contigs Represented = 98
Non ambiguous bp:
Initial: 30009235 bp
After Masking: 16927270 bp
Masked: 43.59 %
-- Input Database Coverage: 40034992 bp out of 2189995079 bp ( 1.83 % )
Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 290703
Comparison Time: 00:22:55 (hh:mm:ss) Elapsed Time, 66435 HSPs Collected
Number of families returned by RECON: 4965
Round Time: 00:35:27 (hh:mm:ss) Elapsed Time : 148 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:12:13 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:03:17 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
237445 repeats masked totaling 41730920 bp(s).
- TE Masking time 00:02:35 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90042728 bp
Num Contigs Represented = 236
Non ambiguous bp:
Initial: 90038528 bp
After Masking: 47350189 bp
Masked: 47.41 %
-- Input Database Coverage: 130077720 bp out of 2189995079 bp ( 5.94 % )
Sampling Time: 00:18:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2618616
Comparison Time: 02:39:14 (hh:mm:ss) Elapsed Time, 262066 HSPs Collected
Number of families returned by RECON: 13988
Round Time: 03:27:38 (hh:mm:ss) Elapsed Time : 506 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:36:06 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:07:50 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
792494 repeats masked totaling 137065887 bp(s).
- TE Masking time 00:11:25 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270039902 bp
Num Contigs Represented = 530
Non ambiguous bp:
Initial: 270029102 bp
After Masking: 130176455 bp
Masked: 51.79 %
-- Input Database Coverage: 400117622 bp out of 2189995079 bp ( 18.27 % )
Sampling Time: 00:55:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23512653
Comparison Time: 16:53:30 (hh:mm:ss) Elapsed Time, 567199 HSPs Collected
Number of families returned by RECON: 43873
Round Time: 20:28:16 (hh:mm:ss) Elapsed Time : 1131 families discovered.
RepeatScout/RECON discovery complete: 2551 families found
Classification Time: 01:16:57 (hh:mm:ss) Elapsed Time
Program Time: 26:26:11 (hh:mm:ss) Elapsed Time