Hi, I am trying to assemble RNAseq data using Trinity on the cluster, but the process failed after 12 hours when it could not make any more folders due to a "Disk quota exceeded" error. What can be done to fix it?
This is the command I'm using: Trinity --genome_guided_bam accepted_hits_filt_sort.bam --genome_guided_max_intron 2000 --max_memory 10G --CPU 10
Thanks in advance for any help you can provide
You have exceeded the maximum number of files in your project (6.674 millions of files > quota 6 millions).
$ lfs quota -h -p 162375 /shared/projects/helmo
Disk quotas for prj 162375 (pid 162375):
Filesystem used quota limit grace files quota limit grace
4.242T 5.859T 8.789T - 6674044* 6000000 9000000 none
So you have to clean your directory.
We can also rise your quota but I would like to be sure that it's necessary.
thank you for your prompt reply. I can delete some files from my space, but I don't think that will be enough, and I need to run another 10 trinity analysis like that, and then I will have to do gene annotation and orthologous gene analysis with several species, and this kind of analysis produces, although small, a lot of files.
I look forward to your reply, thanks
Most of the files are in "busco" directory (3.2 millions of files in
buscoFiles and 2.9M in
There are many directories with thousands of
Maybe there is a way to reduce the
fna files ?
After you run, you might concatenate, compress or archive this directory to reduce the number of files.
Ok,I'll try that, and later on if I need to increase the limit I'll ask for help again.
Thank you so much
Perfect. Of course, come back to us to increase if needed.