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SPAdes error when trying to specify options for path

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

spades
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written by AINUR FATIN BINTI MAZRI • AINUR FATIN BINTI MAZRI

2 answers

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.

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written by Mensur Dlakic Mensur Dlakic

I suspect it is

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

and not

 1  ./Documents/AINUR/MYD/MYD_1.clean.fq
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by AINUR FATIN BINTI MAZRI • AINUR FATIN BINTI MAZRI

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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