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SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error with metagenome assembly using PacBio library #452

Closed kimnegrette3 closed 4 years ago

kimnegrette3 commented 4 years ago

Hi! I am trying to perform a metagenome assembly with SPAdes v3.14.0. I only have seven PacBio Filtered Subreads merged in a single fastq. This is the command line I used:

spades.py --meta --pacbio -s /hpcfs/home/Filtered_Subreads_Fastq/merged1.fastq -t 8 --only-assembler -m 60 -o /hpcfs/home/metaSPADES/PACBIO

This is the error I get:

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: /hpcfs/home/Filtered_Subreads_Fastq/merged1.fastq

I really appreciate any help. Thank you!

asl commented 4 years ago

Hello

First of all, I doubt that 7 pacbio reads contains a metagenome or a part of it.

Further more, per http://cab.spbu.ru/files/release3.14.0/manual.html#sec3.1:

To run SPAdes 3.14.0 you need at least one library of the following types:

kimnegrette3 commented 4 years ago

Thanks for your prompt answer. It is a very small metagenome, four or five species, one of them eukaryote. As suggested, I used CCS reads this time: spades.py --meta --s1 /hpcfs/home/CCS_Reads_Fastq/merged.ccs.fastq -t 8 --only-assembler -m 60 -o /hpcfs/home/metaSPADES/PACBIO_CCS

and I got this 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!

How should I modify the command to rum with this type of files? Thanks!

asl commented 4 years ago

Well, if you're only having 7 reads and 4 or 5 species, then you do not need assembler at all – simply assign reads to species and you're done, there is nothing to assemble here.

Per error message, metaSPAdes allows only hybrid assemblies with Illumina + PacBio data.

kimnegrette3 commented 4 years ago

Sorry for the misunderstanding... I have seven sequencing runs (seven PacBio SMRT-cells), no seven reads.

As you said, we can not use metaSPAdes with only PacBio data. Thank you for the advice.

To solve this issue, do you think we could use one of the next approaches?:

  1. Run metaSPAdes using our PacBio data and include a small data set of illumina sequencing just to simulate having a hybrid sequencing
  2. Run just SPAdes (no meta) with our PacBio data. May these approaches give us good results?

Many regards.

AgustinPardo commented 4 years ago

Hello, I join the conversation because I am trying to use SPAdes(metaSPAdes) with the same type of data (PacBio sequencing). I find myself with the same problem. Do you think the solutions that @kimnegrette3 proposed (1,2) could be usefull?

Regards from Argentina