RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.MRWkSa/RM_20609.MonDec40112252023
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: 1701681143
Database = /dev/shm/rModeler.MRWkSa/GCA_030867105.1_rLiaOli1.hap1 - Sequences = 43
- Bases = 1486119866
Storage Throughput = excellent ( 1166.72 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40043160 bp ( 40002760 non ambiguous )
- Num Contigs Represented = 17
- Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:19:40 (hh:mm:ss) Elapsed Time
Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 315 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
10052 repeats masked totaling 2250867 bp(s).
- TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10040600 bp
Num Contigs Represented = 16
Non ambiguous bp:
Initial: 10000500 bp
After Masking: 7539003 bp
Masked: 24.61 %
-- Input Database Coverage: 10040600 bp out of 1486119866 bp ( 0.68 % )
Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31375
Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 20541 HSPs Collected
Number of families returned by RECON: 1421
Round Time: 00:08:12 (hh:mm:ss) Elapsed Time : 28 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
33017 repeats masked totaling 7223107 bp(s).
- TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30002480 bp
Num Contigs Represented = 17
Non ambiguous bp:
Initial: 30002180 bp
After Masking: 21977042 bp
Masked: 26.75 %
-- Input Database Coverage: 40043080 bp out of 1486119866 bp ( 2.69 % )
Sampling Time: 00:04:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 280875
Comparison Time: 00:31:05 (hh:mm:ss) Elapsed Time, 43043 HSPs Collected
Number of families returned by RECON: 4073
Round Time: 00:37:12 (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 : 00:07:46 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
112600 repeats masked totaling 25114000 bp(s).
- TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90015813 bp
Num Contigs Represented = 19
Non ambiguous bp:
Initial: 90004015 bp
After Masking: 62636729 bp
Masked: 30.41 %
-- Input Database Coverage: 130058893 bp out of 1486119866 bp ( 8.75 % )
Sampling Time: 00:13:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2532375
Comparison Time: 03:34:33 (hh:mm:ss) Elapsed Time, 157778 HSPs Collected
Number of families returned by RECON: 12944
Round Time: 04:53:47 (hh:mm:ss) Elapsed Time : 343 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:23:28 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:09:27 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
397428 repeats masked totaling 87969663 bp(s).
- TE Masking time 00:08:31 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270034850 bp
Num Contigs Represented = 22
Non ambiguous bp:
Initial: 270017663 bp
After Masking: 175031647 bp
Masked: 35.18 %
-- Input Database Coverage: 400093743 bp out of 1486119866 bp ( 26.92 % )
Sampling Time: 00:41:55 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 22798128
Comparison Time: 26:32:27 (hh:mm:ss) Elapsed Time, 393907 HSPs Collected
Number of families returned by RECON: 45569
Round Time: 28:17:36 (hh:mm:ss) Elapsed Time : 771 families discovered.
RepeatScout/RECON discovery complete: 1552 families found
Classification Time: 01:11:16 (hh:mm:ss) Elapsed Time
Program Time: 35:36:23 (hh:mm:ss) Elapsed Time