Question: blast FATAL ERROR: BlastFormattingInfoNew returned non-z
gravatar for rotmus0
5.6 years ago by
European Union
rotmus00 wrote:


I'm running blast commands from a cluster of nodes and sometimes if succeeding and sometimes it fails.

the command i run is:

blastall -p blastn -g F -q -9999 -i ""/users/pmrotem/projects/mirna/hornstein/LB912/qc/LB912.filtered_fastqc/mir_qc//temp/split.1.fasta"" -d ""/bio/db/blast/nt"" -e 0.01 -m 7 -v 1 -b 1 -o ""/users/pmrotem/projects/mirna/hornstein/LB912/qc/LB912.filtered_fastqc/mir_qc//temp/split.1.xml""

<font face="monospace">the error i get is:</font>

WARNING: Unable to open output file /users/pmrotem/projects/mirna/hornstein/LB912/qc/LB912.filtered_fastqc/mir_qc//temp/split.1.xml:
[blastall] FATAL ERROR: BlastFormattingInfoNew returned non-zero status'

after it fails i run the same command without the cluster and it succeds.

can anyone tell about this error?

blast • 1.8k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 5.6 years ago by rotmus00

Try referring to /home/users instead of /users...

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Asaf7.0k

I think that this is a problem with your cluster configuration (you didn't tell us anything relevant about your cluster) that you should discuss with your local cluster admins, it could be so many things, most likely the path does not exist or is not mounted on all nodes. It also might be an automounter problem under NFS, to check simply run `ls /my/output/path` in your cluster script before blast to force automount and exit if that command doesn't find the directory.

On the other hand, normally file not found will result in a 'file not found' message. Maybe your process requires a lot of RAM and you are sometimes getting low-mem nodes? Simply ask your friendly help-desk.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Michael Dondrup47k
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