RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.36Tnhf/RM_2578701.FriSep120608422025
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: 1757682521
Database = /data/tmp/rModeler.36Tnhf/GCA_038502045.1_ASM3850204v1 
  - Sequences = 86
  - Bases = 2896287
Storage Throughput = excellent ( 1584.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 2896163 bp ( 2895780 non ambiguous )
   - Num Contigs Represented = 86
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 12, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 10 families remaining
   - RepeatScout: 00:00:58 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 10 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:09 (hh:mm:ss) Elapsed Time : 7 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 00:00:41 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       189 repeats masked totaling 56718 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2896163 bp
       Num Contigs Represented = 86
       Non ambiguous bp:
             Initial: 2895780 bp
             After Masking: 2679628 bp
             Masked: 7.46 % 
 -- Input Database Coverage: 2896163 bp out of 2896287 bp ( 100.00 % )
Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 9316
Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 2197 HSPs Collected
Number of families returned by RECON: 237
Round Time: 00:05:24 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 9 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.36Tnhf/RM_2578701.FriSep120608422025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:06:42 (hh:mm:ss) Elapsed Time