dRep: Argument list too long

[jianhuang525]

My MAGs have 71,000 bins. it too many~
when i run
dRep dereplicate drep/ -g test/*.fa -sa 0.95 -nc 0.30 -p 256 -pa 0.9 -cm larger
it error
dRep: Argument list too long

how can i cope with it >.<

[MrOlm]

You can provide a text file listing the location of each genome to the -f argument; that way it will get around the argument limit of your system.

Best,
Matt

[jianhuang525]

You can provide a text file listing the location of each genome to the -f argument; that way it will get around the argument limit of your system.

Best, Matt

when i make the genome list , it seed the same error.
ls refinem/*fa > bin_list.txt
-bash: /usr/bin/ls: Argument list too long
i will try to batch settlement to make genome list.

[MrOlm]

You’ll just need to use “find” rather than “ls” to make the genome list.

Best,
Matt