RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.25Lcmb/RM_2527760.MonApr212241402025
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: 1745300499
Database = /data/tmp/rModeler.25Lcmb/GCA_041753875.1_ASM4175387v1 - Sequences = 24
- Bases = 714975658
Storage Throughput = excellent ( 1487.76 MB/s )
RepeatModeler Round # 1
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Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40005290 bp ( 40005290 non ambiguous )
- Num Contigs Represented = 24
- Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:09:46 (hh:mm:ss) Elapsed Time
Round Time: 00:14:25 (hh:mm:ss) Elapsed Time : 366 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:02 (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...
6049 repeats masked totaling 758727 bp(s).
- TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10000918 bp
Num Contigs Represented = 24
Non ambiguous bp:
Initial: 10000918 bp
After Masking: 8973558 bp
Masked: 10.27 %
-- Input Database Coverage: 10000918 bp out of 714975658 bp ( 1.40 % )
Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31125
Comparison Time: 00:03:11 (hh:mm:ss) Elapsed Time, 11881 HSPs Collected
Number of families returned by RECON: 1905
Round Time: 00:03:53 (hh:mm:ss) Elapsed Time : 26 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
20994 repeats masked totaling 3043033 bp(s).
- TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30004336 bp
Num Contigs Represented = 24
Non ambiguous bp:
Initial: 30004336 bp
After Masking: 26036452 bp
Masked: 13.22 %
-- Input Database Coverage: 40005254 bp out of 714975658 bp ( 5.60 % )
Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 281625
Comparison Time: 00:17:15 (hh:mm:ss) Elapsed Time, 61463 HSPs Collected
Number of families returned by RECON: 6595
Round Time: 00:19:50 (hh:mm:ss) Elapsed Time : 130 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
78161 repeats masked totaling 11564437 bp(s).
- TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90026805 bp
Num Contigs Represented = 24
Non ambiguous bp:
Initial: 90026805 bp
After Masking: 75857662 bp
Masked: 15.74 %
-- Input Database Coverage: 130032059 bp out of 714975658 bp ( 18.19 % )
Sampling Time: 00:03:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2532375
Comparison Time: 01:54:34 (hh:mm:ss) Elapsed Time, 285471 HSPs Collected
Number of families returned by RECON: 22097
Round Time: 02:04:53 (hh:mm:ss) Elapsed Time : 523 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:09:19 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
312123 repeats masked totaling 48247986 bp(s).
- TE Masking time 00:04:30 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270003749 bp
Num Contigs Represented = 24
Non ambiguous bp:
Initial: 270003749 bp
After Masking: 213448296 bp
Masked: 20.95 %
-- Input Database Coverage: 400035808 bp out of 714975658 bp ( 55.95 % )
Sampling Time: 00:14:42 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 22804881
Comparison Time: 13:14:06 (hh:mm:ss) Elapsed Time, 909587 HSPs Collected
Number of families returned by RECON: 81294
Round Time: 14:25:03 (hh:mm:ss) Elapsed Time : 1172 families discovered.
RepeatScout/RECON discovery complete: 2217 families found
Classification Time: 00:51:26 (hh:mm:ss) Elapsed Time
Program Time: 17:59:30 (hh:mm:ss) Elapsed Time