Problem Converting BAM to SAM on to Amazon S3 Using Samtools

[foolishbrat]

In my Amazon EC2 instance I have the following:

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:

/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

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:

samtools view -h ~/bar-something-data/myfile.bam > ~/bar-something-data/test.sam

It gave the following error:

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?

[gringer]

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.