In my Amazon EC2 instance I have the following:
ubuntu@ip-333-31-16-230:~$ 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-foolishbrat-data
The last two file system `bar-bi` and `bar-foolishbrat` are Amazon S3 bucket
<https://aws.amazon.com/documentation/s3/>,
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 using Samtools, 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?
Regards,
G.V.
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