=================================
 Project Summary
---------------------------------
# Project Information
  Project Name         : Pgenerosa_v074
  Owner                : kubu4
  Create Date          : 2019-07-09 14:07:39

# Project Properties
  Genus                : Panopea
  Species              : generosa
  Project Type         : invertebrate
  Prefix               : PGEN_
  Common Name          : Pacific geoduck
  Genetic Code         : Standard Code

# Input FASTA
  Filename           : Pgenerosa_v074.fa
  Filesize           : 913.68 MB
  Number of Sequence : 18

=================================
 Job Information
---------------------------------
# Official Gene Set
  >PASA Refinement
  - version : 2.3.3
  - Transcripts FASTA file : Trinity.fasta

  # The source Job of the refinement job
    >Augustus-01
    - version : 3.3.1
    - Species : fly
    - Report genes on : both
    - Allowed gene structure : partial
    - cDNA (transcripts) sequences : Trinity.fasta
    - Protein sequences : 20180827_trinity_geoduck.fasta.transdecoder.fa


# The consensus mask Job
  >Masked Repeat Consensus

  # The source jobs for consensus mask job
    >RepeatMasker
    >RepeatModeler

  # Family copy number summary
    Family	Copy Numbers
    DNA	675
    DNA/Academ	1327
    DNA/Crypton	344
    DNA/Ginger	130
    DNA/Kolobok-T2	141
    DNA/Maverick	942
    DNA/MuLE-MuDR	201
    DNA/MuLE-NOF?	142
    DNA/P	167
    DNA/PIF-Harbinger	227
    DNA/RC	587
    DNA/Sola	508
    DNA/TcMar-Fot1	117
    DNA/TcMar-Mariner	6734
    DNA/TcMar-Tc1	3718
    DNA/hAT-Tip100	516
    DNA/hAT-hAT5	1037
    Type:DNA	17513
    LINE	883
    LINE/CR1	5204
    LINE/CR1-Zenon	14653
    LINE/I	980
    LINE/I-Nimb	1119
    LINE/L1	4031
    LINE/L1-Tx1	6620
    LINE/L2	8879
    LINE/L2-Hydra	113
    LINE/Penelope	1026
    LINE/RTE-X	21214
    Type:LINE	64722
    SINE/tRNA-Core-L2	41152
    Type:SINE	41152
    LTR/Caulimovirus	140
    LTR/DIRS	448
    LTR/Gypsy	1031
    LTR/Ngaro	343
    LTR/Pao	82
    Type:LTR	2044
    Type:EVERYTHING_TE	125431
    Type:Simple_repeat	19235
    Type:Unknown	1465471

# The functional Jobs on the OGS
  >InterProScan
  - version : 5.29-68.0

  >Pfam
  - version : 1.6
  - E-value Sequence : 1
  - E-value Domain : 10

  >SignalP
  - version : 4.1
  - Organism group : euk
  - Method : best
  - D-cutoff for SignalP-noTM networks : 0.45
  - D-cutoff for SignalP-TM networks : 0.50
  - Minimal predicted signal peptide length : 10
  - Truncate to sequence length : 70

  >BLAST protein vs protein (blastp)_SP01
  - version : 2.7.1
  - Protein Data Set : SwissProt
  - Maximum HSP Distinace : 30000
  - Output type : tab
  - Matrix : BLOSUM62
  - Expect : 1e-8
  - Word Size : 3
  - Gap Open : 11
  - Gap Extend : 1

  >DIAMOND Functional_SP01
  - version : 0.9.22
  - Protein Data Set : SwissProt

  >BLAST protein vs protein (blastp)
  - version : 2.7.1
  - Protein Data Set : 20180827_trinity_geoduck.fasta.transdecoder.fa
  - Maximum HSP Distinace : 30000
  - Output type : tab
  - Matrix : BLOSUM62
  - Expect : 1e-8
  - Word Size : 3
  - Gap Open : 11
  - Gap Extend : 1

  >DIAMOND Functional
  - version : 0.9.22
  - Protein Data Set : 20180827_trinity_geoduck.fasta.transdecoder.fa