could not set up reference database for DIAMOND

lulit

New member
Hi,
I have assembled metagenome data and I wanted to perform translated DNA searches using DIAMOND. Last year I used diamond/0.9.11 to align the contigs using 'sensitive mode' and had no problem setting the reference database. However, when I tried to set the reference database using makedb for the latest version (i.e. diamond/0.9.24), the process is killed.
#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database file: nr.gz
Opening the database file... [0.00202s]
Loading sequences... Killed

In addition, when I switched to the older version of diamond (i.e. diamond/0.9.12), what I get is:
#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database file: nr.gz
Opening the database file... [0.026429s]
Loading sequences... Bus error

Is there an alternative nr. gz database for diamond/0.9.24 that I need to download besides wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz?
or am I missing something?

Regards,
 

lulit

New member
I'm remotely working on Brown Oscar server and I don't think I've space problem. However, when I check the free space on my dedicated server what I get is;
[lwolde@node416 ~]$ df -h
Filesystem Size Used Avail Use% Mounted on
rootfs 32G 7.5G 25G 24% /
devtmpfs 32G 0 32G 0% /dev
tmpfs 48G 0 48G 0% /dev/shm
tmpfs 32G 121M 32G 1% /run
tmpfs 32G 0 32G 0% /sys/fs/cgroup
rw 32G 4.0K 32G 1% /.sllocal/log
gpfs 1.1P 834T 243T 78% /gpfs
home 20T 11T 9.1T 54% /gpfs_home
mgt5:/install 259G 176G 70G 72% /install
oscarcnfs:/gpfs/scratch 1.1P 834T 243T 78% /nfs/scratch
oscarcnfs:/gpfs/data 1.1P 834T 243T 78% /nfs/data
tmpfs 6.3G 0 6.3G 0% /run/user/0
 

Benjamin Buchfink

Administrator
Staff member
Could you try to run any other program on this system that needs a couple GB of memory and reads/writes large files? Does this work?
 
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