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!
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>
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.
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
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
By the way, you should use Add comment or Add reply when responding to previous answer or a comment rather than creating a new answer.
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