RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bwCW3V/RM_2614494.FriSep121828242025
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1757726903
Database = /dev/shm/rModeler.bwCW3V/GCA_051312685.1_HcG217B_UCSF2 
  - Sequences = 8
  - Bases = 39487987
Storage Throughput = excellent ( 1616.30 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39487974 bp ( 39487974 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 74 raw families identified
   - RepeatScout: Running filtering stage.. 69 families remaining
   - RepeatScout: 00:03:34 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 68 families... 00:07:29 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 6 satellite(s), 18 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:11:09 (hh:mm:ss) Elapsed Time : 46 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2801 repeats masked totaling 2379976 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10009892 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10009892 bp
             After Masking: 7523747 bp
             Masked: 24.84 % 
 -- Input Database Coverage: 10009892 bp out of 39487987 bp ( 25.35 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:03:31 (hh:mm:ss) Elapsed Time, 35757 HSPs Collected
Number of families returned by RECON: 364
Round Time: 00:04:54 (hh:mm:ss) Elapsed Time : 11 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (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...
       7859 repeats masked totaling 10335156 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29478077 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 29478077 bp
             After Masking: 18819012 bp
             Masked: 36.16 % 
 -- Input Database Coverage: 39487969 bp out of 39487987 bp ( 100.00 % )
Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 273430
Comparison Time: 00:12:35 (hh:mm:ss) Elapsed Time, 7652 HSPs Collected
Number of families returned by RECON: 1495
Round Time: 00:14:04 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 71 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bwCW3V/RM_2614494.FriSep121828242025
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:29 (hh:mm:ss) Elapsed Time


Program Time: 00:30:36 (hh:mm:ss) Elapsed Time