RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BHCSak/RM_1774.FriMay122258172023
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: 1683957495
Database = /dev/shm/rModeler.BHCSak/GCA_900324485.3_fMasArm1.3 - Sequences = 123
- Bases = 591951591
- N50 = 25822229
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
27182527-29124071 |*** [ 6 ]
25240984-27182527 |** [ 4 ]
23299441-25240984 |** [ 4 ]
21357898-23299441 |* [ 3 ]
19416355-21357898 |** [ 5 ]
17474812-19416355 | [ ]
15533269-17474812 | [ 1 ]
13591725-15533268 | [ ]
11650182-13591725 | [ ]
9708639-11650182 | [ 1 ]
7767096-9708639 | [ ]
5825553-7767096 | [ ]
3884010-5825553 | [ ]
1942467-3884010 |* [ 3 ]
924-1942467 |************************************************** [ 96 ]
Storage Throughput = excellent ( 1130.71 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40979963 bp ( 40007433 non ambiguous )
- Num Contigs Represented = 43
- Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:19:42 (hh:mm:ss) Elapsed Time
Round Time: 00:24:28 (hh:mm:ss) Elapsed Time : 264 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
3947 repeats masked totaling 1237325 bp(s).
- TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10398108 bp
Num Contigs Represented = 31
Non ambiguous bp:
Initial: 10011095 bp
After Masking: 8623103 bp
Masked: 13.86 %
-- Input Database Coverage: 10398108 bp out of 591951591 bp ( 1.76 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 33670
Comparison Time: 00:07:06 (hh:mm:ss) Elapsed Time, 5184 HSPs Collected
Number of families returned by RECON: 1111
Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 10 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:25 (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...
12685 repeats masked totaling 3498300 bp(s).
- TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30661801 bp
Num Contigs Represented = 37
Non ambiguous bp:
Initial: 30037975 bp
After Masking: 26128685 bp
Masked: 13.01 %
-- Input Database Coverage: 41059909 bp out of 591951591 bp ( 6.94 % )
Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 295296
Comparison Time: 00:38:49 (hh:mm:ss) Elapsed Time, 30074 HSPs Collected
Number of families returned by RECON: 4381
Round Time: 00:41:48 (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 : 00:01:15 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
43903 repeats masked totaling 12068778 bp(s).
- TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 92031257 bp
Num Contigs Represented = 64
Non ambiguous bp:
Initial: 90014207 bp
After Masking: 76691158 bp
Masked: 14.80 %
-- Input Database Coverage: 133091166 bp out of 591951591 bp ( 22.48 % )
Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2683086
Comparison Time: 04:38:22 (hh:mm:ss) Elapsed Time, 202307 HSPs Collected
Number of families returned by RECON: 18379
Round Time: 04:58:35 (hh:mm:ss) Elapsed Time : 333 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:09:10 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
175423 repeats masked totaling 44309838 bp(s).
- TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 276132669 bp
Num Contigs Represented = 93
Non ambiguous bp:
Initial: 270002686 bp
After Masking: 221952016 bp
Masked: 17.80 %
-- Input Database Coverage: 409223835 bp out of 591951591 bp ( 69.13 % )
Sampling Time: 00:21:55 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23995128
Comparison Time: 36:20:20 (hh:mm:ss) Elapsed Time, 679496 HSPs Collected
Number of families returned by RECON: 78312
Round Time: 38:59:09 (hh:mm:ss) Elapsed Time : 860 families discovered.
RepeatScout/RECON discovery complete: 1521 families found
Classification Time: 01:28:35 (hh:mm:ss) Elapsed Time
Program Time: 46:40:36 (hh:mm:ss) Elapsed Time