SPAdes error when trying to specify options for path

Question

[AINUR FATIN BINTI MAZRI]

Hi,

I cannot figure out how to solve this problem. I have read other posts fot this issue but I am still getting this error.

spades.py -k 127 --careful -1 --pe-1 1 ./Documents/AINUR/MYD/MYD_1.clean.fq -2 --pe-1 2 ./Documents/AINUR/MYD/MYD_2.clean.fq -o ./Documents/AINUR/MYD/spades_MYD_output_denovo_assembly -t 16 


== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths: 1, ./Documents/AINUR/MYD/MYD_1.clean.fq, 2, ./Documents/AINUR/MYD/MYD_2.clean.fq

I am not sure what it meant by specify options, hoping someone can help.

Thank you

Answer 1

[Mensur Dlakic]

You are using multiple options by specifying -1 --pe-1 1 and -2 --pe-1 2. These are not supposed to be combined.

If you have two files with single reads (seems to be the case here), the command would be:

spades.py -k 127 --careful -1 ./Documents/AINUR/MYD/MYD_1.clean.fq -2 ./Documents/AINUR/MYD/MYD_2.clean.fq -o ./Documents/AINUR/MYD/spades_MYD_output_denovo_assembly -t 16

If you have multiple libraries with single reads (doesn't seem to be the case here), the command would be:

spades.py -k 127 --careful --pe-1 1 ./Documents/AINUR/MYD/MYD_1.clean.fq --pe-1 2 ./Documents/AINUR/MYD/MYD_2.clean.fq -o ./Documents/AINUR/MYD/spades_MYD_output_denovo_assembly -t 16

Even though the second command might also run, there is no reason to specify multiple libraries if you only have two files of single reads, as that amounts to only one library.

[AINUR FATIN BINTI MAZRI]

Thank you for this, sir. It does work! Thank you so much.

Answer 2

[Pierre Lindenbaum]

I suspect it is

 -1  ./Documents/AINUR/MYD/MYD_1.clean.fq

and not

 1  ./Documents/AINUR/MYD/MYD_1.clean.fq

[AINUR FATIN BINTI MAZRI]

I already tried the -1, but it still doesn't work.

spades.py -k 127 --careful -1 --pe1-1 /home/colfax/Documents/AINUR/MYD/MYD_1.clean.fq -2 --pe1-2 /home/colfax/Documents/AINUR/MYD/MYD_2.clean.fq -o .home/colfax/Documents/AINUR/MYD/spades_MYD_output_denovo_assembly -t 16

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: /home/colfax/Documents/AINUR/MYD/MYD_1.clean.fq, /home/colfax/Documents/AINUR/MYD/MYD_2.clean.fq

[Pierre Lindenbaum]

there is no option -1 in your command above. I can see --pe1-1 but not -1