RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.3b8GZZ/RM_1206493.SatMar291723032025
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: 1743294181
Database = /data/tmp/rModeler.3b8GZZ/GCA_048569485.1_aAnoBae1.hap1 - Sequences = 3642
- Bases = 6265077250
- N50 = 707846305
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
911955041-977094522 | [ 1 ]
846815561-911955041 | [ ]
781676081-846815561 | [ 1 ]
716536601-781676081 | [ ]
651397121-716536601 | [ 2 ]
586257641-651397121 | [ 1 ]
521118161-586257641 | [ 1 ]
455978681-521118161 | [ ]
390839201-455978681 | [ ]
325699721-390839201 | [ ]
260560241-325699721 | [ 2 ]
195420761-260560241 | [ 3 ]
130281281-195420761 | [ 1 ]
65141801-130281281 | [ ]
2321-65141801 |************************************************** [ 3630 ]
Storage Throughput = fair ( 697.41 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40017119 bp ( 40011119 non ambiguous )
- Num Contigs Represented = 103
- Sequence extraction : 00:06:01 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:11:51 (hh:mm:ss) Elapsed Time
Round Time: 00:28:10 (hh:mm:ss) Elapsed Time : 987 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
16741 repeats masked totaling 5518173 bp(s).
- TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10033466 bp
Num Contigs Represented = 33
Non ambiguous bp:
Initial: 10032166 bp
After Masking: 2717479 bp
Masked: 72.91 %
-- Input Database Coverage: 10033466 bp out of 6265077250 bp ( 0.16 % )
Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31878
Comparison Time: 00:04:05 (hh:mm:ss) Elapsed Time, 11220 HSPs Collected
Number of families returned by RECON: 1051
Round Time: 00:08:44 (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 : 00:04:32 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
49496 repeats masked totaling 16949978 bp(s).
- TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30023573 bp
Num Contigs Represented = 82
Non ambiguous bp:
Initial: 30018873 bp
After Masking: 7966788 bp
Masked: 73.46 %
-- Input Database Coverage: 40057039 bp out of 6265077250 bp ( 0.64 % )
Sampling Time: 00:10:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 286146
Comparison Time: 00:13:45 (hh:mm:ss) Elapsed Time, 44804 HSPs Collected
Number of families returned by RECON: 3141
Round Time: 00:24:29 (hh:mm:ss) Elapsed Time : 95 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:13:35 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:16:04 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
162754 repeats masked totaling 52576668 bp(s).
- TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90037511 bp
Num Contigs Represented = 198
Non ambiguous bp:
Initial: 90026611 bp
After Masking: 23032862 bp
Masked: 74.42 %
-- Input Database Coverage: 130094550 bp out of 6265077250 bp ( 2.08 % )
Sampling Time: 00:31:37 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2584401
Comparison Time: 01:00:18 (hh:mm:ss) Elapsed Time, 241398 HSPs Collected
Number of families returned by RECON: 8060
Round Time: 01:35:45 (hh:mm:ss) Elapsed Time : 438 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:40:19 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:47:27 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
530835 repeats masked totaling 169319672 bp(s).
- TE Masking time 00:06:44 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270035746 bp
Num Contigs Represented = 506
Non ambiguous bp:
Initial: 270004945 bp
After Masking: 55783565 bp
Masked: 79.34 %
-- Input Database Coverage: 400130296 bp out of 6265077250 bp ( 6.39 % )
Sampling Time: 01:34:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23348361
Comparison Time: 05:47:11 (hh:mm:ss) Elapsed Time, 784175 HSPs Collected
Number of families returned by RECON: 18362
Round Time: 07:36:41 (hh:mm:ss) Elapsed Time : 1079 families discovered.
RepeatScout/RECON discovery complete: 2617 families found
Classification Time: 01:02:16 (hh:mm:ss) Elapsed Time
Program Time: 11:16:05 (hh:mm:ss) Elapsed Time