RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.hsSM17/RM_2349788.FriSep121845142025
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: 1757727913
Database = /data/tmp/rModeler.hsSM17/GCA_051313235.1_HcG217B_UCSF3 
  - Sequences = 8
  - Bases = 39481474
Storage Throughput = excellent ( 1234.57 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39481383 bp ( 39481383 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:04 (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: 00:06:57 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 68 families... 00:12:32 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 4 satellite(s), 17 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time
Round Time: 00:19:39 (hh:mm:ss) Elapsed Time : 47 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 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2480 repeats masked totaling 2343547 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029096 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 10029096 bp
             After Masking: 7583512 bp
             Masked: 24.38 % 
 -- Input Database Coverage: 10029096 bp out of 39481474 bp ( 25.40 % )
Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:04:26 (hh:mm:ss) Elapsed Time, 29627 HSPs Collected
Number of families returned by RECON: 375
Round Time: 00:07:32 (hh:mm:ss) Elapsed Time : 8 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 00:00:52 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8176 repeats masked totaling 10255037 bp(s).
   - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29452207 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 29452207 bp
             After Masking: 18870993 bp
             Masked: 35.93 % 
 -- Input Database Coverage: 39481303 bp out of 39481474 bp ( 100.00 % )
Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 271953
Comparison Time: 00:15:42 (hh:mm:ss) Elapsed Time, 7105 HSPs Collected
Number of families returned by RECON: 1519
Round Time: 00:17:15 (hh:mm:ss) Elapsed Time : 16 families discovered.

RepeatScout/RECON discovery complete: 71 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.hsSM17/RM_2349788.FriSep121845142025
# 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: 00:00:33 (hh:mm:ss) Elapsed Time


Program Time: 00:44:59 (hh:mm:ss) Elapsed Time