RepeatModeler Version 2.0.4
===========================
Using output directory = /scratch/tmp/rModeler.UndZAl/RM_1123841.SunNov170632462024
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: 1731853966
Database = /scratch/tmp/rModeler.UndZAl/GCA_011762505.2_mArvNil1.pat.X - Sequences = 1596
- Bases = 2496777707
- N50 = 86386494
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
155975538-167116563 | [ 1 ]
144834513-155975537 | [ 1 ]
133693489-144834513 | [ 2 ]
122552464-133693488 | [ 1 ]
111411440-122552464 | [ ]
100270415-111411439 | [ 2 ]
89129390-100270414 | [ 1 ]
77988366-89129390 | [ 6 ]
66847341-77988365 | [ 3 ]
55706317-66847341 | [ 1 ]
44565292-55706316 | [ 7 ]
33424267-44565291 | [ 2 ]
22283243-33424267 | [ 4 ]
11142218-22283242 | [ 1 ]
1194-11142218 |************************************************** [ 1564 ]
Storage Throughput = excellent ( 1481.68 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40309840 bp ( 40005344 non ambiguous )
- Num Contigs Represented = 97
- Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:07:29 (hh:mm:ss) Elapsed Time
Round Time: 00:13:26 (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 : 00:00:14 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
13795 repeats masked totaling 2688388 bp(s).
- TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10113019 bp
Num Contigs Represented = 47
Non ambiguous bp:
Initial: 10003091 bp
After Masking: 6848355 bp
Masked: 31.54 %
-- Input Database Coverage: 10113019 bp out of 2496777707 bp ( 0.41 % )
Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 32640
Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 76959 HSPs Collected
Number of families returned by RECON: 832
Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 12 families discovered.
RepeatModeler Round # 3
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 30000000 bp
- Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
42552 repeats masked totaling 8060474 bp(s).
- TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30196810 bp
Num Contigs Represented = 82
Non ambiguous bp:
Initial: 30002242 bp
After Masking: 20681808 bp
Masked: 31.07 %
-- Input Database Coverage: 40309829 bp out of 2496777707 bp ( 1.61 % )
Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 297606
Comparison Time: 00:14:53 (hh:mm:ss) Elapsed Time, 126279 HSPs Collected
Number of families returned by RECON: 2686
Round Time: 00:18:49 (hh:mm:ss) Elapsed Time : 49 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
133142 repeats masked totaling 25285696 bp(s).
- TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90988663 bp
Num Contigs Represented = 144
Non ambiguous bp:
Initial: 90010333 bp
After Masking: 61028435 bp
Masked: 32.20 %
-- Input Database Coverage: 131298492 bp out of 2496777707 bp ( 5.26 % )
Sampling Time: 00:09:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2639253
Comparison Time: 01:35:08 (hh:mm:ss) Elapsed Time, 1363669 HSPs Collected
Number of families returned by RECON: 9679
Round Time: 01:46:48 (hh:mm:ss) Elapsed Time : 195 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:30:37 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
449762 repeats masked totaling 83377243 bp(s).
- TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 272204169 bp
Num Contigs Represented = 343
Non ambiguous bp:
Initial: 270016379 bp
After Masking: 175324488 bp
Masked: 35.07 %
-- Input Database Coverage: 403502661 bp out of 2496777707 bp ( 16.16 % )
Sampling Time: 00:39:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23739495
Comparison Time: 11:36:00 (hh:mm:ss) Elapsed Time, 17570135 HSPs Collected
Number of families returned by RECON: 38511
Round Time: 12:32:05 (hh:mm:ss) Elapsed Time : 417 families discovered.
RepeatScout/RECON discovery complete: 1039 families found
Classification Time: 00:21:22 (hh:mm:ss) Elapsed Time
Program Time: 15:21:40 (hh:mm:ss) Elapsed Time