In my Amazon EC2 instance I have the following:
The last two file system `bar-bi` and `bar-foolishbrat` are Amazon S3 bucket,
mounted with the following command:
Now I have no problem doing this, in my instance
That is writing the SAM file in my instance file system. But when I do this, namely writing to the mounted S3:
It gave the following error:
How can I resolve this issue? Is there any other tool for converting BAM to SAM other than samtools?
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
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.
Code:
samtools view -h ~/bar-something-data/myfile.bam > test.sam
Code:
samtools view -h ~/bar-something-data/myfile.bam > ~/bar-something-data/test.sam
Code:
samtools: writing to standard output failed: Invalid argument samtools: error closing standard output: -1
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