Disk quota exceeded while running trinity

IFB Core Cluster
#1

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

#2

Hi,

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
/shared/projects/helmo
                 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.

#3

Hi @dbenaben,

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

#4

Most of the files are in "busco" directory (3.2 millions of files in buscoFiles and 2.9M in buscoOutputs)
image

There are many directories with thousands of fna and gff files.

Maybe there is a way to reduce the gffand/or fna files ?
After you run, you might concatenate, compress or archive this directory to reduce the number of files.

#5

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

#6

Perfect. Of course, come back to us to increase if needed.