Error setting up BUSCO for loop
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16 months ago
jamie.pike ▴ 80

I'm having trouble setting up a for loop with BUSCO - I can't see any syntax errors, but I keep getting an error message reporting one. Can anyone see what the issue is?

nohup for i in $(cat BUSCO_list.txt); do busco -m genome -i ../DNA/${i} -o ${i}.BUSCO -l ~/Fusarium_data/Raw_Genomes/BUSCO/sordariomycetes_odb10 ; done &
bash: syntax error near unexpected token `do'
BUSCO for loop BASH Syntax error • 459 views
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Entering edit mode
16 months ago
h.mon 33k

https://stackoverflow.com/questions/3099092/why-cant-i-use-unix-nohup-with-bash-for-loop

In addition, tmux or screen are much better alternatives to nohup. If you are in a cluster environment, you should probably use the queue manager designed by the system administrators

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That's fixed it - great thank you!

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