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Old 05-15-2018, 06:22 AM   #1
k_a_r_o_l
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Default Krona updateAccessions.sh

Hello,

I am trying to do updateAccessions.sh in Krona. Unfortunately during that process (sorting) I don't have enough space in /tmp so everything stops.

Do you have any tips how to run this process avoiding tmp standard directory or running it with temporary "new" tmp directory?

thx
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Old 05-16-2018, 03:38 AM   #2
k_a_r_o_l
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OK. I've found a solution. In a script accession2.taxid.make change the line:

SORT := grep -v accession | sed 's/\.[[:digit:]]*//' | LC_ALL=C sort
to
SORT := grep -v accession | sed 's/\.[[:digit:]]*//' | LC_ALL=C sort -T /home/DIR

As a DIR put any directory with enough space.
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