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  • 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

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