Doubt about specifying options in SPAdes
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6.6 years ago

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 Assembly metagenomics • 3.3k views
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The input looks OK. Which SPAdes version are you using?

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The version I am using is 3.11.0.

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

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

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

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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?

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

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And what is the output of:

ls -lh /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq
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-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
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6.5 years ago
maxwhjohn1988 ▴ 130

Try:

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

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Same error is still occuring.

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