RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.uepqvE/RM_3888432.WedFeb110156582026
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: 1770803818
Database = /data/tmp/rModeler.uepqvE/GCA_035232765.1_ASM3523276v1 
  - Sequences = 8
  - Bases = 9259183
Storage Throughput = fair ( 508.05 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9259044 bp ( 9259042 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 51 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:51 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 9 families... 00:00:31 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time
Round Time: 00:01:27 (hh:mm:ss) Elapsed Time : 5 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 00:00:26 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       133 repeats masked totaling 126202 bp(s).
   - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9259044 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 9259042 bp
             After Masking: 9034597 bp
             Masked: 2.42 % 
 -- Input Database Coverage: 9259044 bp out of 9259183 bp ( 100.00 % )
Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 27495
Comparison Time: 00:07:19 (hh:mm:ss) Elapsed Time, 1011 HSPs Collected
Number of families returned by RECON: 312
Round Time: 00:08:03 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 5 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.uepqvE/RM_3888432.WedFeb110156582026
# 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: 00:00:16 (hh:mm:ss) Elapsed Time


Program Time: 00:09:46 (hh:mm:ss) Elapsed Time