RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.yOKudt/RM_18428.TueJan160245072024
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: 1705401903
Database = /dev/shm/rModeler.yOKudt/GCA_963457625.1_fCycLum2.1 - Sequences = 232
- Bases = 586296809
- N50 = 25165805
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
30161796-32316139 | [ 1 ]
28007453-30161795 | [ 2 ]
25853111-28007453 |* [ 6 ]
23698768-25853110 | [ 4 ]
21544426-23698768 |* [ 5 ]
19390083-21544425 | [ 2 ]
17235740-19390082 | [ 1 ]
15081398-17235740 | [ 2 ]
12927055-15081397 | [ 1 ]
10772713-12927055 | [ 1 ]
8618370-10772712 | [ ]
6464027-8618369 | [ ]
4309685-6464027 | [ ]
2155342-4309684 | [ ]
1000-2155342 |************************************************** [ 207 ]
Storage Throughput = excellent ( 1047.74 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40012061 bp ( 40000661 non ambiguous )
- Num Contigs Represented = 38
- Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:22:50 (hh:mm:ss) Elapsed Time
Round Time: 00:30:32 (hh:mm:ss) Elapsed Time : 282 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 00:02:27 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
4066 repeats masked totaling 785182 bp(s).
- TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10003679 bp
Num Contigs Represented = 26
Non ambiguous bp:
Initial: 10001679 bp
After Masking: 8114336 bp
Masked: 18.87 %
-- Input Database Coverage: 10003679 bp out of 586296809 bp ( 1.71 % )
Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31125
Comparison Time: 00:08:04 (hh:mm:ss) Elapsed Time, 7238 HSPs Collected
Number of families returned by RECON: 1322
Round Time: 00:11:14 (hh:mm:ss) Elapsed Time : 15 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:07:06 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
13566 repeats masked totaling 2553121 bp(s).
- TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30048366 bp
Num Contigs Represented = 37
Non ambiguous bp:
Initial: 30038966 bp
After Masking: 23978979 bp
Masked: 20.17 %
-- Input Database Coverage: 40052045 bp out of 586296809 bp ( 6.83 % )
Sampling Time: 00:07:56 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 285390
Comparison Time: 00:37:38 (hh:mm:ss) Elapsed Time, 39057 HSPs Collected
Number of families returned by RECON: 4692
Round Time: 00:47:11 (hh:mm:ss) Elapsed Time : 73 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:21:35 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
46156 repeats masked totaling 8392100 bp(s).
- TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90069063 bp
Num Contigs Represented = 64
Non ambiguous bp:
Initial: 90035863 bp
After Masking: 70911809 bp
Masked: 21.24 %
-- Input Database Coverage: 130121108 bp out of 586296809 bp ( 22.19 % )
Sampling Time: 00:24:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2584401
Comparison Time: 04:03:48 (hh:mm:ss) Elapsed Time, 249072 HSPs Collected
Number of families returned by RECON: 17997
Round Time: 04:52:35 (hh:mm:ss) Elapsed Time : 345 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 01:04:54 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
190932 repeats masked totaling 36534359 bp(s).
- TE Masking time 00:07:58 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270090542 bp
Num Contigs Represented = 133
Non ambiguous bp:
Initial: 270000811 bp
After Masking: 202124620 bp
Masked: 25.14 %
-- Input Database Coverage: 400211650 bp out of 586296809 bp ( 68.26 % )
Sampling Time: 01:16:53 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23225520
Comparison Time: 31:46:49 (hh:mm:ss) Elapsed Time, 870570 HSPs Collected
Number of families returned by RECON: 68618
Round Time: 34:59:25 (hh:mm:ss) Elapsed Time : 856 families discovered.
RepeatScout/RECON discovery complete: 1571 families found
Classification Time: 01:18:21 (hh:mm:ss) Elapsed Time
Program Time: 42:39:18 (hh:mm:ss) Elapsed Time