RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.Wf2CcF/RM_3200082.SunMay40829042025
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: 1746372541
Database = /data/tmp/rModeler.Wf2CcF/GCA_037953035.1_aLitCat1_p1.0 - Sequences = 4071
- Bases = 6623830220
- N50 = 4277981
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
32043264-34330989 | [ 1 ]
29755540-32043264 | [ ]
27467815-29755539 | [ 1 ]
25180091-27467815 | [ ]
22892367-25180091 | [ ]
20604642-22892366 | [ 1 ]
18316918-20604642 | [ 6 ]
16029193-18316917 | [ 5 ]
13741469-16029193 | [ 17 ]
11453745-13741469 | [ 23 ]
9166020-11453744 | [ 35 ]
6878296-9166020 |* [ 98 ]
4590571-6878295 |*** [ 204 ]
2302847-4590571 |******** [ 521 ]
15123-2302847 |************************************************** [ 3159 ]
Storage Throughput = excellent ( 1087.01 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40015510 bp ( 40015510 non ambiguous )
- Num Contigs Represented = 748
- Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:12:21 (hh:mm:ss) Elapsed Time
Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 1048 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 00:01:12 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
19277 repeats masked totaling 5186477 bp(s).
- TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10010746 bp
Num Contigs Represented = 232
Non ambiguous bp:
Initial: 10010746 bp
After Masking: 4091502 bp
Masked: 59.13 %
-- Input Database Coverage: 10010746 bp out of 6623830220 bp ( 0.15 % )
Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31878
Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 13318 HSPs Collected
Number of families returned by RECON: 1618
Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 19 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 00:03:26 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
56974 repeats masked totaling 15720389 bp(s).
- TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30004684 bp
Num Contigs Represented = 601
Non ambiguous bp:
Initial: 30004684 bp
After Masking: 12056374 bp
Masked: 59.82 %
-- Input Database Coverage: 40015430 bp out of 6623830220 bp ( 0.60 % )
Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 286903
Comparison Time: 00:20:20 (hh:mm:ss) Elapsed Time, 68498 HSPs Collected
Number of families returned by RECON: 4947
Round Time: 00:31:55 (hh:mm:ss) Elapsed Time : 128 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:11:06 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
180032 repeats masked totaling 49361306 bp(s).
- TE Masking time 00:02:51 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90023235 bp
Num Contigs Represented = 1274
Non ambiguous bp:
Initial: 90023235 bp
After Masking: 33832112 bp
Masked: 62.42 %
-- Input Database Coverage: 130038665 bp out of 6623830220 bp ( 1.96 % )
Sampling Time: 00:14:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2593503
Comparison Time: 01:47:04 (hh:mm:ss) Elapsed Time, 372195 HSPs Collected
Number of families returned by RECON: 13593
Round Time: 02:39:56 (hh:mm:ss) Elapsed Time : 616 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:31:34 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
610383 repeats masked totaling 169817433 bp(s).
- TE Masking time 00:12:56 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270016504 bp
Num Contigs Represented = 2073
Non ambiguous bp:
Initial: 270016504 bp
After Masking: 79565346 bp
Masked: 70.53 %
-- Input Database Coverage: 400055169 bp out of 6623830220 bp ( 6.04 % )
Sampling Time: 00:45:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23314206
Comparison Time: 10:51:36 (hh:mm:ss) Elapsed Time, 1006465 HSPs Collected
Number of families returned by RECON: 31745
Round Time: 13:49:17 (hh:mm:ss) Elapsed Time : 1584 families discovered.
RepeatScout/RECON discovery complete: 3395 families found
Classification Time: 01:54:08 (hh:mm:ss) Elapsed Time
Program Time: 19:31:57 (hh:mm:ss) Elapsed Time