missing file on R component about irap HOT 5 CLOSED

This could be the same issue as I had, where /dev/shm (a ramdisk) is to small to hold the gtf file (my gtf file was 1.3 gb. In my case I increased /dev/shm from 1 to 4 GB and solved it. What size is your /dev/shm? (Output of: mount | grep /dev/shm)

from irap.

Hi Pete,

I looked at the irap.txt file and is a bit difficult to understand the first lines, namely the line one where irap env. variables are defined by running "source irap_setup.sh". Did you run this command once before running irap?

Cheers.

from irap.

Hi again,
Looking more carefully at the log file I noticed that there was an I/O problem upstream.

'...
Loading gtf file /opt/irap_install/data/reference/homo_sapiens/ensembl.gtf
grep: write error'

Maybe the storage is full?

Cheers.

from irap.

from irap.

Hi,
There should not be necessary to create any file manually - that would void the purpose of having a pipeline ;-)
The problem should be on the temporary folder (usually /tmp or other tmpfs folder setup on your computer node) used while uncompressing the input file and not on the toplevel folder. The function that loads the data determines the temporary folder to use by checking the environment variables TMPDIR, TMP and TEMP in turn and the first found which points to a writable directory is used: if none succeeds /tmp is used. Does this make sense?

Cheers.

from irap.