RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.wHLILd/RM_293493.ThuSep110227142025
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: 1757582833
Database = /data/tmp/rModeler.wHLILd/GCA_022605425.2_FIOER33_v3 
  - Sequences = 17
  - Bases = 21638905
Storage Throughput = good ( 873.08 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 21638773 bp ( 21638773 non ambiguous )
   - Num Contigs Represented = 17
   - 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.. : 145 raw families identified
   - RepeatScout: Running filtering stage.. 126 families remaining
   - RepeatScout: 00:02:34 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 118 families... 00:03:56 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 44 contained, found in 00:00:15 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:15 (hh:mm:ss) Elapsed Time
Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 74 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 00:01:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5643 repeats masked totaling 3689097 bp(s).
   - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10004972 bp
       Num Contigs Represented = 17
       Non ambiguous bp:
             Initial: 10004972 bp
             After Masking: 6122470 bp
             Masked: 38.81 % 
 -- Input Database Coverage: 10004972 bp out of 21638905 bp ( 46.24 % )
Sampling Time: 00:03:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:12:49 (hh:mm:ss) Elapsed Time, 7091 HSPs Collected
Number of families returned by RECON: 454
Round Time: 00:16:59 (hh:mm:ss) Elapsed Time : 7 families discovered.
   - Increasing sample size to include end piece now = 41638905


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 41638905 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6796 repeats masked totaling 4875116 bp(s).
   - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 11633780 bp
       Num Contigs Represented = 17
       Non ambiguous bp:
             Initial: 11633780 bp
             After Masking: 6535753 bp
             Masked: 43.82 % 
 -- Input Database Coverage: 21638752 bp out of 21638905 bp ( 100.00 % )
Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43365
Comparison Time: 00:13:52 (hh:mm:ss) Elapsed Time, 2076 HSPs Collected
Number of families returned by RECON: 448
Round Time: 00:18:06 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 85 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.wHLILd/RM_293493.ThuSep110227142025
# 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: 00:02:52 (hh:mm:ss) Elapsed Time


Program Time: 00:44:48 (hh:mm:ss) Elapsed Time