Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problem with velveth

    I am experiencing a very peculiar problem with velvet version 0.7.45 – results for the same input data are different under different conditions. I used a live sequence data (file my_sequence.txt) from a next generation shotgun sequencer – the data I received is in zip format (viz., my_sequence.txt.zip). The statement of the problem is as following.
    1. When I use the velveth program on the zip data with file format fastq.gz, the zip sequence file is processed successfully by velveth with 167555 sequences found in the file.
    2. When I use the same file in velveth with file format fastq instead of fastq.gz, the file is processed normally without any error and the result is same with 167555 sequences found. As I used the wrong file type, I was expecting velveth to terminate with an error, but velveth processed it successfully.
    3. I then useed the unzip utility to unzip the file from my_sequence.txt.zip to my_sequence.txt. The unzipped file is stored in the local directory by default.
    4. I run velveth on the unzipped sequence file (my_sequence.txt) using file format as fastq.gz by mistake instead of fastq file format. Surprisingly velveth does not throw any error; instead, it processes the unzipped file successfully with file format fastq.gz. Surprise enough, it now finds 991278 sequences, which is much higher (about 6 times) compared to the previous run on the zipped data for the same file.
    5. Just being curious, I run velveth on the unzipped file once again, but this time I correct the file format – I use the file format as fastq; however, instead of running successfully, velveth throws error my_sequence.txt incomplete.: No such file or directory

    We will appreciate if anyone could explain such behavior that looks inconsistent. The complete operational sequence is listed here.

    asoke@asoke-laptop:~/velvet/velvet_0.7.45$ ./velveth sillyDirectory 21 -fastq -short ../../data/my_sequence.txt.zip
    Reading FastQ file ../../data/my_sequence.txt.zip
    167555 reads found.
    Done
    Reading read set file sillyDirectory/Sequences;
    167555 sequences found
    Done
    167555 sequences in total.
    Writing into roadmap file sillyDirectory/Roadmaps...
    Inputting sequences...
    Inputting sequence 0 / 167555
    Inputting sequence 100000 / 167555
    Done inputting sequences
    Destroying splay table
    Splay table destroyed
    asoke@asoke-laptop:~/velvet/velvet_0.7.45$ ./velveth sillyDirectory 21 -fastq.gz -short ../../data/my_sequence.txt.zip
    Reading FastQ file ../../data/my_sequence.txt.zip
    167555 reads found.
    Done
    Reading read set file sillyDirectory/Sequences;
    167555 sequences found
    Done
    167555 sequences in total.
    Writing into roadmap file sillyDirectory/Roadmaps...
    Inputting sequences...
    Inputting sequence 0 / 167555
    Inputting sequence 100000 / 167555
    Done inputting sequences
    Destroying splay table
    Splay table destroyed
    asoke@asoke-laptop:~/velvet/velvet_0.7.45$ unzip ../../data/my_sequence.txt.zip
    Archive: ../../data/my_sequence.txt.zip
    inflating: my_sequence.txt
    asoke@asoke-laptop:~/velvet/velvet_0.7.45$ ./velveth sillyDirectory 21 -fastq.gz -short my_sequence.txt
    Reading FastQ file my_sequence.txt
    991278 reads found.
    Done
    Reading read set file sillyDirectory/Sequences;
    991278 sequences found
    Done
    991278 sequences in total.
    Writing into roadmap file sillyDirectory/Roadmaps...
    Inputting sequences...
    Inputting sequence 0 / 991278
    Inputting sequence 100000 / 991278
    Inputting sequence 200000 / 991278
    Inputting sequence 300000 / 991278
    Inputting sequence 400000 / 991278
    Inputting sequence 500000 / 991278
    Inputting sequence 600000 / 991278
    Inputting sequence 700000 / 991278
    Inputting sequence 800000 / 991278
    Inputting sequence 900000 / 991278
    Done inputting sequences
    Destroying splay table
    Splay table destroyed
    asoke@asoke-laptop:~/velvet/velvet_0.7.45$ ./velveth sillyDirectory 21 -fastq -short my_sequence.txt
    Reading FastQ file my_sequence.txt
    velveth: my_sequence.txt incomplete.: No such file or directory
    asoke@asoke-laptop:~/velvet/velvet_0.7.45$

  • #2
    Please post bugs and problems with Velvet to the Velvet mailing list.



    The author, Daniel Zerbino, is active on the list, and there are many other people who could help.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-14-2024, 06:13 AM
    0 responses
    32 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-08-2024, 08:03 AM
    0 responses
    71 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-07-2024, 08:13 AM
    0 responses
    80 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-06-2024, 09:51 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X