Re: [wgs-assembler-users] Oxford Nanopore/Illumina Sequence error

[Serge K. <ser...@gm...>]

Hi,

As listed on the documentation for PBcR, there is no support for Illumina-based correction of Oxford data:
“While PBcR supports high-identity data for correction, this mode is no longer being updated, is not supported for MinION data, and is significantly slower than self-correction due to its reliance on BLASR (or a built-in module) for overlap computation."

You can only perform the self-correction using only oxford data. Just remove the frg file from your PBcR command and it should run.

Sergey

> On Apr 1, 2015, at 10:15 AM, Stephen Taylor <ste...@im...> wrote:
> 
> Hi,
> 
> I am trying to assemble some Oxford Nanopore reads with Illumina PE Sequences  using PBcR (8.3rc2). 
> 
> So I prepare the Illumina sequences like this
> 
> fastqToCA -libraryname illumina_paired_end -technology illumina -type sanger -mates Lamp_R1_001.fastq,Lamp_R2_001.fastq -insertsize 200 50 > illumina_paired_end.frg
> 
> and then do the assembly thus:
> 
> PBcR -length 500 -partitions 200 -libraryname lamp60 -s oxford.spec -fastq exp16.fastq -genomeSize 60000 illumina_paired_end.frg 
> 
> But I get
> 
> Error: The PacBio library 0 must be the last library loaded but it preceedes 1. Please double-check your input files and try again. at /package/wgs/8.3rc2/Linux-amd64/bin/PBcR line 1470.
> 
> I notice this error had been posted before but I think mine is different  since ' illumina_paired_end' is the illumina library name and ' lamp60' is the assembled library name so there shouldn't be a conflict.
> 
> http://sourceforge.net/p/wgs-assembler/mailman/wgs-assembler-users/?viewmonth=201307
> 
> Please can some give me some idea what I should do?
> 
> Kind regards and thanks,
> 
> Steve
> 
> 
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