Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    ABYSS pe error

    Hello, I got this error message from ABYSS -pe

    error: removing `contigs-0.fa': No such file or directory

    What should I do to make it works?

    Thank you.
    Tags: None
  • #2
    Give us more information on how you are running ABySS. This is not a common error.

    Comment

    • #3
      This is the command that I used:

      /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'



      This is how the end of the logfile looks like:


      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-bubbles.fa
      Done.
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory

      ===================================================================================
      = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
      = PID 62249 RUNNING AT gntcs-alit-hp1
      = EXIT CODE: 9
      = CLEANING UP REMAINING PROCESSES
      = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
      ===================================================================================
      YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
      This typically refers to a problem with your application.
      Please see the FAQ page for debugging suggestions
      make: *** [testtest-1.fa] Error 15
      -bash-4.1$

      Comment

      • #4
        This is the command I used:

        /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hise/abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'q/PE2P.fastq'


        This is the tail of the logfile:
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-1.fa
        0: Assembled 355161061 k-mer in 7443983 contigs.
        Assembled 355161061 k-mer in 7443983 contigs.
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-bubbles.fa
        Done.
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory

        ===================================================================================
        = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
        = PID 62249 RUNNING AT gntcs-alit-hp1
        = EXIT CODE: 9
        = CLEANING UP REMAINING PROCESSES
        = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
        ===================================================================================
        YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
        This typically refers to a problem with your application.
        Please see the FAQ page for debugging suggestions
        make: *** [testtest-1.fa] Error 15
        -bash-4.1$

        Comment

        • #5
          I ran it remotely using this command

          /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hise/abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'q/PE2P.fastq'

          This is the tail of the log file

          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-1.fa
          0: Assembled 355161061 k-mer in 7443983 contigs.
          Assembled 355161061 k-mer in 7443983 contigs.
          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-bubbles.fa
          Done.
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory

          ===================================================================================
          = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
          = PID 62249 RUNNING AT gntcs-alit-hp1
          = EXIT CODE: 9
          = CLEANING UP REMAINING PROCESSES
          = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
          ===================================================================================
          YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
          This typically refers to a problem with your application.
          Please see the FAQ page for debugging suggestions
          make: *** [testtest-1.fa] Error 15
          -bash-4.1$

          Comment

          Previous template Next

          Latest Articles

          Collapse
          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • 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
          View All

          ad_right_rmr

          Collapse

          News

          Collapse
          Topics Statistics Last Post
          Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          30 views
          0 likes
          		 Last Post seqadmin
          by seqadmin
          04-11-2024, 12:08 PM  
          Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          32 views
          0 likes
          		 Last Post seqadmin
          by seqadmin
          04-10-2024, 10:19 PM  
          Novel Diagnostic Assay Enhances Ovarian Cancer Detection by seqadmin
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          28 views
          0 likes
          		 Last Post seqadmin
          by seqadmin
          04-10-2024, 09:21 AM  
          Evolutionary Dynamics of Centromeres: A Comparative Genomic Analysis by seqadmin
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          52 views
          0 likes
          		 Last Post seqadmin
          by seqadmin
          04-04-2024, 09:00 AM  
          View All
          Working...
          X