Doubt about specifying options in SPAdes

Question

[inaciogmedeiros]

I've tried to run SPAdes with following command:

$ spades/bin/spades.py -s input.fastq --iontorrent --only-assembler --careful  -o output.result

However, following error message occurs:

== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths: /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq, :

In case you have troubles running SPAdes, you can write to [e-mail] or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.

My questions are:

1. I have setted "s" flag (see "-s input.fastq") (it's a single-ended fastq file). Why does still SPAdes gives this error?
2. Which is the correct manner, in this case, to run SPAdes?

[Asaf]

The input looks OK. Which SPAdes version are you using?

[inaciogmedeiros]

The version I am using is 3.11.0.

[inaciogmedeiros]

An additional detail: argument for --s1 is a absolute path for input.fastq. Does this make any substantial difference?

[inaciogmedeiros]

spades script is also being called via absolute path, from another external path from spades.

[GenoMax]

As long as the paths are correct, it should not matter if they are relative or full.

[h.mon]

Why the error message complains about /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq, if you use just -s input.fastq?

[inaciogmedeiros]

Command I've posted was a "model" of how I'm using SPAdes (I've ended up forgetting to adapt error message, sorry).

[h.mon]

And what is the output of:

ls -lh /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq

[inaciogmedeiros]

-rw-r--r--. 1 inacio binfo 3,6K Set 28 11:49 /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq

Answer 1

[maxwhjohn1988]

Try:

spades.py --s1 input.fastq ... <other options="">

[inaciogmedeiros]

Same error is still occuring.