Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problem Converting BAM to SAM on to Amazon S3 Using Samtools

    In my Amazon EC2 instance I have the following:

    Code:
    ubuntu@ip-133-31-16-230:~$ df -h
    Filesystem       Size  Used Avail Use% Mounted on
    udev              79G     0   79G   0% /dev
    tmpfs             16G  8.8M   16G   1% /run
    /dev/xvda1       985G  136G  809G  15% /
    tmpfs             79G     0   79G   0% /dev/shm
    tmpfs            5.0M     0  5.0M   0% /run/lock
    tmpfs             79G     0   79G   0% /sys/fs/cgroup
    tmpfs             16G     0   16G   0% /run/user/1000
    bar-something  1.0P     0  1.0P   0% /home/ubuntu/bar-something-data
    bar-foolishbrat  1.0P     0  1.0P   0% /home/ubuntu/bar-foolisbrat-data
    The last two file system `bar-bi` and `bar-foolishbrat` are Amazon S3 bucket,
    mounted with the following command:

    Code:
    /home/ubuntu/go/bin/goofys bar-foolishbrat bar-foolishbrat-data
    /home/ubuntu/go/bin/goofys bar-somehting bar-something-data
    # Here we use Goofys. It can be achieved also with S3FS.
    Now I have no problem doing this, in my instance

    Code:
    samtools view -h ~/bar-something-data/myfile.bam > test.sam
    That is writing the SAM file in my instance file system. But when I do this, namely writing to the mounted S3:

    Code:
    samtools view -h ~/bar-something-data/myfile.bam > ~/bar-something-data/test.sam
    It gave the following error:

    Code:
    samtools: writing to standard output failed: Invalid argument
    samtools: error closing standard output: -1
    How can I resolve this issue? Is there any other tool for converting BAM to SAM other than samtools?
    Last edited by foolishbrat; 02-20-2017, 05:35 PM.

  • #2
    Is there any other tool for converting BAM to SAM other than samtools?
    Ignoring the obvious "... why?"

    Probably, but why would you want to use a spoon to dig yourself out of a hole when the excavator is still there?

    The most recent versions of the samtools packages allow writing directly to files ('-o <fileName>'), which may fix the output redirect issue you have. I don't know for sure, because I've never played around with EC2.

    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
    34 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-08-2024, 08:03 AM
    0 responses
    72 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-07-2024, 08:13 AM
    0 responses
    81 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