RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.qmA9f6/RM_2144798.FriApr112314252025
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: 1744438464
Database = /data/tmp/rModeler.qmA9f6/GCA_964374135.1_mGraGri1.hap1.1 - Sequences = 1146
- Bases = 2667081928
- N50 = 110541855
- Contig Histogram:
Size(bp) Count
-----------------------------------------------------------------------
171112037-183334296 | [ 3 ]
158889779-171112037 | [ ]
146667520-158889778 | [ ]
134445262-146667520 | [ 2 ]
122223004-134445262 | [ 1 ]
110000745-122223003 | [ 3 ]
97778487-110000745 | [ 3 ]
85556228-97778486 | [ 5 ]
73333970-85556228 | [ 2 ]
61111712-73333970 | [ ]
48889453-61111711 | [ 2 ]
36667195-48889453 | [ 1 ]
24444936-36667194 | [ ]
12222678-24444936 | [ 1 ]
420-12222678 |************************************************** [ 1123 ]
Storage Throughput = excellent ( 1433.92 MB/s )
RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 40028252 bp ( 40025252 non ambiguous )
- Num Contigs Represented = 142
- Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
- RepeatScout: 00:11:07 (hh:mm:ss) Elapsed Time
Round Time: 00:18:34 (hh:mm:ss) Elapsed Time : 169 families discovered.
RepeatModeler Round # 2
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 10000000 bp
- Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
8804 repeats masked totaling 2665011 bp(s).
- TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10008981 bp
Num Contigs Represented = 50
Non ambiguous bp:
Initial: 10008381 bp
After Masking: 6967988 bp
Masked: 30.38 %
-- Input Database Coverage: 10008981 bp out of 2667081928 bp ( 0.38 % )
Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 31626
Comparison Time: 00:04:04 (hh:mm:ss) Elapsed Time, 133777 HSPs Collected
Number of families returned by RECON: 817
Round Time: 00:06:29 (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 : 00:00:49 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:04:35 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
30135 repeats masked totaling 10259032 bp(s).
- TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 30019191 bp
Num Contigs Represented = 118
Non ambiguous bp:
Initial: 30016791 bp
After Masking: 18831733 bp
Masked: 37.26 %
-- Input Database Coverage: 40028172 bp out of 2667081928 bp ( 1.50 % )
Sampling Time: 00:05:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 285390
Comparison Time: 00:19:04 (hh:mm:ss) Elapsed Time, 44114 HSPs Collected
Number of families returned by RECON: 2313
Round Time: 00:25:13 (hh:mm:ss) Elapsed Time : 59 families discovered.
RepeatModeler Round # 4
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 90000000 bp
- Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:05:32 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
102178 repeats masked totaling 32349400 bp(s).
- TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 90023539 bp
Num Contigs Represented = 220
Non ambiguous bp:
Initial: 90014536 bp
After Masking: 55142767 bp
Masked: 38.74 %
-- Input Database Coverage: 130051711 bp out of 2667081928 bp ( 4.88 % )
Sampling Time: 00:09:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 2584401
Comparison Time: 01:51:08 (hh:mm:ss) Elapsed Time, 161126 HSPs Collected
Number of families returned by RECON: 8214
Round Time: 02:02:06 (hh:mm:ss) Elapsed Time : 176 families discovered.
RepeatModeler Round # 5
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 270000000 bp
- Sequence extraction : 00:06:53 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
- TRFMask time 00:11:58 (hh:mm:ss) Elapsed Time
-- Masking repeats from the previous rounds...
342480 repeats masked totaling 105216758 bp(s).
- TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 270063142 bp
Num Contigs Represented = 492
Non ambiguous bp:
Initial: 270038321 bp
After Masking: 157368985 bp
Masked: 41.72 %
-- Input Database Coverage: 400114853 bp out of 2667081928 bp ( 15.00 % )
Sampling Time: 00:21:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
- Total Comparisons = 23211891
Comparison Time: 10:11:23 (hh:mm:ss) Elapsed Time, 2312020 HSPs Collected
Number of families returned by RECON: 32197
Round Time: 10:44:58 (hh:mm:ss) Elapsed Time : 345 families discovered.
RepeatScout/RECON discovery complete: 764 families found
Classification Time: 00:16:52 (hh:mm:ss) Elapsed Time
Program Time: 13:54:12 (hh:mm:ss) Elapsed Time