No output nr file after running makedb
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3.4 years ago
Chvatil ▴ 60

I'm actually trying to creat a database for diamond with this script:

#PBS -S /bin/bash
#PBS -l nodes=1:ppn=2
#PBS -e /pandata/me/blast_database/makedb.error
#PBS -o /pandata/me/blast_database/makedb.out
#PBS -N makedb2
#PBS -q q1hour
hostname
uname -a

echo debut:
date  #debut 

diamond=/panhome/me/miniconda3/bin/diamond 

nr_faa=/pandata/me/blast_database/nr.faa

$diamond makedb --in $nr_faa -d nr2

So I ran it an it actually worked without error (makedb.error file is empty) but I cannot find the nr2 outfile nowhere and I do not know why? It ran on a cluster. Thank for your help.

blast diamond makedb • 1.6k views
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As I recall DIAMOND needs a lot of memory. You don't seem to have specified any additional beyond your default allocation. I will need to look this up but I may have used 80G or so last time I made the indexes.

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With 30 GB is not enought? because I already ran it with less that that, here I do not understand why it does not work. I'll try with :bigmem,mem=30gb and let you know

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Hi still get the same probleme, everything seems to work but I cannot see the file, if. it was a memory probleme I should get an error message no?

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Do you have write permissions on the directory where you are running this job from? Since you are not specifying an output directory/path, DIAMOND will try to write nr2 to the current directory.

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Well, if I do $diamond makedb --in $nr_faa -d directory/path/nr2 will it work? or it accepts aonly a name?

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Try to see if it already present somewhere else on your system by using @h.mon's suggestion.

Otherwise try the command above. That file should be 60+G so you are not going to miss it.

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What is the output of stdout and stderr? Did you try to find the diamond db:

find ~ -name "nr2.dmnd"
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This command does not work, when I use it with a file name that exists, nothing appends (I'm in a virtual env - server)

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nothing appends

Do you mean "nothing happens"? That command is doing a search with that file name.

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Toto26 : You may still be working on/through this question.

In case the question has been solved then indicate which of the following comments was useful (or if you found an independent solution then post that as an answer). I can move that comment to an answer so it can be accepted.

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