RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.i4Cjer/RM_2673117.SunFeb92111032025
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: 1739164261
Database = /data/tmp/rModeler.i4Cjer/GCA_965113325.1_fLeuLeu2.hap2.1 - Sequences = 530
- Bases = 1179019172
- N50 = 44970170
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
78195265-83780570 | [ 1 ]
72609960-78195264 | [ ]
67024656-72609960 | [ 1 ]
61439351-67024655 | [ 1 ]
55854046-61439350 | [ ]
50268742-55854046 | [ 2 ]
44683437-50268741 | [ 5 ]
39098132-44683436 | [ 8 ]
33512828-39098132 | [ 5 ]
27927523-33512827 | [ 2 ]
22342218-27927522 | [ ]
16756914-22342218 | [ ]
11171609-16756913 | [ ]
5586304-11171608 | [ ]
1000-5586304 |************************************************** [ 505 ]
Storage Throughput = excellent ( 1520.56 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40038499 bp ( 40029699 non ambiguous )
- Num Contigs Represented = 61
- Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:08:56 (hh:mm:ss) Elapsed Time
Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 1256 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 00:00:52 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
16109 repeats masked totaling 3649206 bp(s).
- TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10010810 bp
Num Contigs Represented = 34
Non ambiguous bp:
Initial: 10008410 bp
After Masking: 5749775 bp
Masked: 42.55 %
-- Input Database Coverage: 10010810 bp out of 1179019172 bp ( 0.85 % )
Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31626
Comparison Time: 00:04:27 (hh:mm:ss) Elapsed Time, 7584 HSPs Collected
Number of families returned by RECON: 1806
Round Time: 00:05:58 (hh:mm:ss) Elapsed Time : 11 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
48833 repeats masked totaling 10913481 bp(s).
- TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30027609 bp
Num Contigs Represented = 53
Non ambiguous bp:
Initial: 30021209 bp
After Masking: 17529404 bp
Masked: 41.61 %
-- Input Database Coverage: 40038419 bp out of 1179019172 bp ( 3.40 % )
Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 283881
Comparison Time: 00:18:15 (hh:mm:ss) Elapsed Time, 87782 HSPs Collected
Number of families returned by RECON: 5633
Round Time: 00:23:25 (hh:mm:ss) Elapsed Time : 140 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:07:49 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
157490 repeats masked totaling 34154936 bp(s).
- TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90049248 bp
Num Contigs Represented = 111
Non ambiguous bp:
Initial: 90034248 bp
After Masking: 51029590 bp
Masked: 43.32 %
-- Input Database Coverage: 130087667 bp out of 1179019172 bp ( 11.03 % )
Sampling Time: 00:11:43 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2582128
Comparison Time: 01:49:24 (hh:mm:ss) Elapsed Time, 879719 HSPs Collected
Number of families returned by RECON: 16200
Round Time: 02:10:13 (hh:mm:ss) Elapsed Time : 746 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:25:23 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
561236 repeats masked totaling 124163369 bp(s).
- TE Masking time 00:14:02 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270059300 bp
Num Contigs Represented = 244
Non ambiguous bp:
Initial: 270008196 bp
After Masking: 131138278 bp
Masked: 51.43 %
-- Input Database Coverage: 400146967 bp out of 1179019172 bp ( 33.94 % )
Sampling Time: 00:43:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23259610
Comparison Time: 11:49:41 (hh:mm:ss) Elapsed Time, 3728031 HSPs Collected
Number of families returned by RECON: 41895
Round Time: 13:17:19 (hh:mm:ss) Elapsed Time : 1696 families discovered.
RepeatScout/RECON discovery complete: 3849 families found
Classification Time: 01:50:38 (hh:mm:ss) Elapsed Time
Program Time: 18:05:33 (hh:mm:ss) Elapsed Time