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No space left on device error with deeptools bamCompare

Hello! I'm running a few scripts right now on a server and whenever I run bamCompare I get the 'no space left of device' error.

$ df -H
Filesystem      Size  Used Avail Use% Mounted on
/dev/xvda1       16G   16G     0 100% /
none            4.0K     0  4.0K   0% /sys/fs/cgroup
udev             16G  4.0K   16G   1% /dev
tmpfs           3.2G  380K  3.2G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none             16G     0   16G   0% /run/shm
none            100M     0  100M   0% /run/user
/dev/xvdf        30G   29G  1.2M 100% /software
/dev/xvdg       985G  748G  196G  80% /data

After the error occurs I am also unable to tab-complete and I get this error message:

-bash: cannot create temp file for here-document: No space left on device

Looking in the /tmp/ directory (size 848KB), it is filled with files that look like this

-rw-------  1 ubuntu ubuntu 4.6M Jul 17 11:25 _deeptools_szwlxqn_.bg

Restarting the server fixes the 'no space left' error, but it will simply happen again if I try to run bamCompare on my files. I hope someone knows what might be going on here. I'm clearly not very experienced with linux. THANK YOU!

software error deeptools picard bash terminal
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updated by Kevin Blighe Kevin Blighe • written by jennxyzhang • jennxyzhang

Your /data/ directory is the one with space for analysis - it has 1TB. Your root directory (/) is mounted on a 16GB device.

What this means is that if you're running analysis outside /data/, (that is, if /tmp/ is being used), you'll run out of space really fast. Try setting the temp folder location in bamCompare (a quick google search says you need to set a parameter in a config file (see here, you will need to dig deeper).

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written by Ram Ram

In other news you also need to make space in your root directory

/dev/xvda1       16G   16G     0 100% /

Some errant file may have been saved there. Look at a listing of / and check.

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written by GenoMax GenoMax

Is it possible to reallocate more space for the root directory? Can't find much to remove..

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written by jennxyzhang • jennxyzhang

Your directory cannot be larger than the disk it sits on. If /dev/xvda1 has 16G capacity only, / cannot be larger. I'm not sure if it is possible to mount the / folder on a different device without reinstalling the OS.

For each folder under / that is mounted on /dev/xvda1, run du -sh. Point the largest (which would also be the one that grows the most, like a data directory or a tmp folder) to a new disk.

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written by Ram Ram

The config parameter is deprecated now, and instead you can just set the environment variable TMPDIR to whatever temporary directory you want.

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written by rpolicastro rpolicastro

1 answer

As per rpolicastro, and for others arriving here with this problem, you can solve this by temporarily changing the TMPDIR location, as follows:

TMPDIR="/Kevin/Projects/analysis/customtemp"
export TMPDIR

This is not permanent and TMPDIR will be restored to its original value once your session ends.

Kevin

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written by Kevin Blighe Kevin Blighe

Unless you add it to your dotfiles....

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written by Joe Joe

If it's only needed by this application, it's easier to not add to the dotfile. In fact, I'd add an alias to the dotfile instead:

function bamCompare {
     export TMPDIR="/custom/temp/directory"
    /path/to/bamCompare "$@"
}
export -f bamCompare
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written by Ram Ram

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