Question: Doubt about specifying options in SPAdes
23 months ago by
inaciogmedeiros • 10
inaciogmedeiros • 10 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 firstname.lastname@example.org 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:
- I have setted "s" flag (see "-s input.fastq") (it's a single-ended fastq file). Why does still SPAdes gives this error?
- Which is the correct manner, in this case, to run SPAdes?
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