Question: Error before creating De Bruin Graphs
gravatar for vshiv
3 months ago by
vshiv0 wrote:


I am running the following command

bin/kissplice -s 1 -k 41 --experimental -r /path/to/read1 -r /path/to/read2

using kissplice-2.4.0-p1 (note: I installed this on my institution's cluster, so I used make install instead of sudo make install)

I am getting an error about 3 minutes after running the above line:

Building de Bruijn graph...
Graph will be written in results/graph_PF01_R1_PF01_R2_k41.[edges/nodes]
estimated values: nbits Bloom 33, nb FP 14511889, max memory 1024 MB
File /tmp/kissplice.R_37HJ/all_read_filenames starts with character "/", hence is interpreted as a list of file names
Reading 2 read files
Available disk space in /path/to/reads: 213243762 MB
error: can't fwrite (disk full?)

taille cell 32 
Sequentially counting ~319864 MB of kmers with 113 partition(s) and 4 passes using 1 thread(s), ~1024 MB of memory and ~83522 MB of disk space

There are 210 Tb of space left on the partition of the cluster I am using, but it still says disk full, can't fwrite.

Any help is appeciated. Thanks!

kissplice • 194 views
ADD COMMENTlink modified 11 weeks ago by leandro.ishi.lima70 • written 3 months ago by vshiv0

Just to confirm - you are using real paths in place of (/path/to/) and have obfuscated them for privacy here.

If true, you do not seem to have write privileges to the folder that you are running this from. Have you looked at kissplice command options to see if you can specify an output location, where your account will have write privileges? I doubt you can use -r twice in a single command line. Check on that option in the command manual as well.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax48k

Yes, I have hidden the real path names of the reads.

I will contact the system admin to see if I have permission to write in this folder. But I did add files to the directory and write some files before, so I believe I do have permission.

I am pretty sure you can use -r twice in the command, since that is taken straight from the kissplice website and tutorial for running the command on multiple sets of reads (for example paired end reads.)

ADD REPLYlink written 3 months ago by vshiv0
gravatar for leandro.ishi.lima
11 weeks ago by
leandro.ishi.lima70 wrote:

Dear vshiv,

Sorry for the late reply. It could be that KisSplice is trying to create temporary files in the /tmp folder, and this partition might not be too big. You can override which temp folder to use by passing the parameter -d:

-d <PATH_TO_TMP>: Specific directory (absolute path) where to build temporary files (default temporary directory otherwise).

Could you please check this and reply if it worked or not?


ADD COMMENTlink written 11 weeks ago by leandro.ishi.lima70

Muito Obrigado amigo! Funcionou comigo.

ADD REPLYlink written 11 weeks ago by vshiv0

De nada! Obrigado pela questão!

ADD REPLYlink written 10 weeks ago by leandro.ishi.lima70
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