Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • InParanoid blastall and formatb ERROR

    Hi everyone!

    I'm trying to find protein orthologs between strains using InParanoid.
    But when I execute it, I obtain errors in <formatdb> and <blast-all> phase.
    Is this normal? Or am I doing something wrong? The command seems simple.
    Thanks in advance!!!


    Command:
    $ perl inparanoid.pl strain1.fa strain2.fa


    Here, a part of the Output with errors:
    Trying to run BLAST now - this may take several hours ... or days in worst case!
    Formatting BLAST databases
    Done formatting
    Starting BLAST searches...

    Starting first BLAST pass for strain1.fa - strain1.fa on mar abr 24 20:53:57 CEST 2018
    [blastall] WARNING: the -C 3 argument is currently experimental


    Starting second BLAST pass for strain1.fa - strain1.fa on mar abr 24 20:54:38 CEST 2018
    [formatdb] WARNING: Cannot add sequence number 1 (lcl|1_./tmpd) because it has zero-length.

    [formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
    [blastall] FATAL ERROR: -triphosphate: Database ./tmpd was not found or does not exist

    no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.
    [formatdb] WARNING: Cannot add sequence number 2 (lcl|2_./tmpd) because it has zero-length.

    [formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
    [blastall] FATAL ERROR: NZ_000411.1_prot_WP_011112711.1_1: Database ./tmpd was not found or does not exist

  • #2
    solved :-)

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X