SAPdes not support single-end data?

Question

[zhangdengwei]

Dear all,

I am using SAPdes to assemble metadata which was single-end sequencing, here is my code nohup metaspades.py --s1 /mnt/microbio_research/dengwei/20200311_FMT/02.remove_host_kneaddata/H1/sub_H1_35000000.fq -t 4 -o ./H1 & And I keep getting the following error

== Error == you cannot specify any data types except a single paired-end library (optionally accompanied by a single library of TSLR-contigs, or PacBio reads, or Nanopore reads) in metaSPAdes mode! 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.

Where the problem occurred? Any suggestion is appreciated. Thanks very much.

Answer 1

[GenoMax]

From SPAdes manual:

Currently metaSPAdes supports only a single short-read library which has to be paired-end

[zhangdengwei]

Thanks. I found the error reminding me of not specifying the data type. After checking the parameters, only IonTorrent/PacBio/Nanopore was supported, whereas data was derived from Illumina. However, SPAde can process Illumina data as it was mentioned in its tutorial. So I am a bit confused again.

[GenoMax]

If you want to use metaSPAdes for metagenomics data then it has to be a pair-end dataset. Use plain SPAdes if you still want to use that package but have single-end data.

[zhangdengwei]

Got it, thanks, I indeed worked.