Spades error when trying to specify options.

Question

[MJ1996]

Hi,

I'm sure this is really simple but can anyone tell me what is wrong in the following line:

spades.py --pe1-1 ./paired_end.1_trimmed.fq.gz --pe1-2  ./paired_end.2_trimmed.fq.gz \ --mp1-1 ./mate_paired.1_trimmed.fq.gz --mp1-2 ./mate_paired.2_trimmed.fq.gz \ -o ./mated_and_paired_ends

I keep getting the following error:

spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths:  --mp1-1, ./mate_paired.1_trimmed.fq.gz,  -o, ./mated_and_paired_ends

But I have already specified an option with --mp1-1?

Thanks!

Answer 1

[Mensur Dlakic]

You need to specify the number (space separated) after the --mp-1 switch (that's the meaning of --mp-1 <#>). The same is true for --pe-1 as that syntax is deprecated.

  --mp-1 <#> <filename>       file with forward reads for mate-pair library number <#>.
                              Older deprecated syntax is -mp<#>-1 <filename>
  --mp-2 <#> <filename>       file with reverse reads for mate-pair library number <#>.
                              Older deprecated syntax is -mp<#>-2 <filename>

Answer 2

[MJ1996]

As in:

---mp1-1 -1 and --mp1-2 -2 ? This returns the following:

spades.py: error: argument --mp1-2: expected 1 argument

[Mensur Dlakic]

As in --mp-1 1 filename and --mp-2 2 filename. Not sure why you are still using --mp1-1 when command options are clearly telling you to use --mp-1.

Answer 3

[MJ1996]

Okay, thanks. In this case I have written the following:

spades.py --pe-1 -1 ./paired_end.1_trimmed.fq.gz --pe-2 -2 ./paired_end.2_trimmed.fq.gz \ --mp-1 -1 ./mate_paired.1_trimmed.fq.gz --mp-2 -2 ./mate_paired.2_trimmed.fq.gz \ -o ./mated_and_paired_ends

And now I get: spades.py: error: argument --pe-1: expected 2 arguments

I'm trying to implement the following (taken directly from the manual) spades.py --pe1-1 lib_pe1_left.fastq --pe1-2 lib_pe1_right.fastq \ --mp1-1 lib_mp1_left.fastq --mp1-2 lib_mp1_right.fastq \ --mp2-1 lib_mp2_left.fastq --mp2-2 lib_mp2_right.fastq \ -o spades_output

[Mensur Dlakic]

I don't mean to be rude, but this is basic reading of what is in front of you on the screen. Why are you putting a negative number (-1 or -2) after --pe-1 or --pe-2 when in all the examples above I was using positive numbers (1 or 2)? It is interpreting those -1 and -2 as command-line switches rather than library numbers, so it doesn't think you provided a library number and complains argument --pe-1: expected 2 arguments.

spades.py --pe-1 1 ./paired_end.1_trimmed.fq.gz --pe-2 2 ./paired_end.2_trimmed.fq.gz --mp-1 1 ./mate_paired.1_trimmed.fq.gz --mp-2 2 ./mate_paired.2_trimmed.fq.gz -o ./mated_and_paired_ends

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