Question: Doubt about specifying options in SPAdes
0
gravatar for inaciogmedeiros
23 months ago by
inaciogmedeiros10 wrote:

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 spades.support@cab.spbu.ru 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?
spades metagenomics assembly • 1.1k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by inaciogmedeiros10

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

ADD REPLYlink written 23 months ago by Asaf6.1k

The version I am using is 3.11.0.

ADD REPLYlink written 23 months ago by inaciogmedeiros10

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

ADD REPLYlink written 23 months ago by inaciogmedeiros10

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

ADD REPLYlink written 23 months ago by inaciogmedeiros10

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

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax70k

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?

ADD REPLYlink written 23 months ago by h.mon27k

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

ADD REPLYlink modified 23 months ago • written 23 months ago by inaciogmedeiros10

And what is the output of:

ls -lh /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq
ADD REPLYlink written 23 months ago by h.mon27k
-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
ADD REPLYlink written 22 months ago by inaciogmedeiros10
0
gravatar for maxwhjohn1988
23 months ago by
maxwhjohn198880 wrote:

Try:

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

ADD COMMENTlink written 23 months ago by maxwhjohn198880

Same error is still occuring.

ADD REPLYlink modified 23 months ago • written 23 months ago by inaciogmedeiros10
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