Hi everybody I`m using spades trying to assembly a trypanosomatid genome, i just have around 150 MB reads from nanopore sequencer, the smallest read its about 150 bp, and the longest about 84 kb, I know that i have no enough reads for genome assembly but I am trying to do it anyway, thats my command line:
spades.py --careful --nanopore --only-assembler -o out_spades -s file.fastq
It does not works, did somebody has used it before?
Thanks!
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written
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Buffo
1 answer
Ok, actually it will only use Nanopore as part of a hybrid assembly. From the docs:
"SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available."
So it's expecting the nanopore reads filename after the --nanopore argument (which explains your error) but it's also expecting another file to do a hybrid assembly.
Do you have Illumina or other data?
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Maybe give the error message or describe how it fails?
== Error == file not found: /home/fcallejas/bug4/mix_b4/--only-assembler (single reads, library number: 2, library type: nanopore)
Post your full command please. It looks like you either have typos or odd characters in your filename (so use quotes)
spades.py --nanopore --only-assembler -o bug_spades -s mix_bug4.fastq
error message == Error == file not found: /home/fcallejas/bug4/mix_b4/--only-assembler (single reads, library number: 2, library type: nanopore)
i`m doing it by tcsh script on cluster.