> From: Sulbha Choudhari [[email protected]]
> Sent: Monday, August 18, 2014 1:26 PM
> To: Boisvert, Sebastien
> Subject: Ray Meta
>
>
>
> Hello Dr. Boisvert,
> I would be thankful if you could help me in the software, Ray Meta generated
> by you.
> I am trying to assemble a metagenome generated by Miseq as paired end
> sequences using meta_ray.
> I am using the following command:
>
>
> srun Ray -k31 -p
> /u1/home/user/data/Miseq/20140602Filter1_S1_L001_R1_001.CutAdaptor.trimed.fasta-common.out2090
> -p
> /u1/home/user/data/Miseq/20140602Filter1_S1_L001_R2_001.CutAdaptor.trimed.fasta-common.out2090
> -o RayOutput_miseq_2090_1
This command is invalid. It has 3 problems:
- there should be a space between -k and 31 ("-k 31").
- the option -p needs 2 or 4 arguments. In your case, that would be:
-p
/u1/home/user/data/Miseq/20140602Filter1_S1_L001_R1_001.CutAdaptor.trimed.fasta-common.out2090
/u1/home/user/data/Miseq/20140602Filter1_S1_L001_R2_001.CutAdaptor.trimed.fasta-common.out2090
- Files with the extension .out2090 are not supported by Ray.
Supported formats are:
Input files
Note: file format is determined with file extension.
.fasta
.fa
.fasta.gz (needs HAVE_LIBZ=y at compilation)
.fa.gz (needs HAVE_LIBZ=y at compilation)
.fasta.bz2 (needs HAVE_LIBBZ2=y at compilation)
.fa.bz2 (needs HAVE_LIBBZ2=y at compilation)
.fastq
.fq
.fastq.gz (needs HAVE_LIBZ=y at compilation)
.fq.gz (needs HAVE_LIBZ=y at compilation)
.fastq.bz2 (needs HAVE_LIBBZ2=y at compilation)
.fq.bz2 (needs HAVE_LIBBZ2=y at compilation)
export.txt
qseq.txt
.sff (paired reads must be extracted manually)
.csfasta (color-space reads)
.csfa (color-space reads)
>
>
>
>
> It runs for few seconds and then it gets terminated and I get error in the
> slurm file :
> Error: -p needs 2 or 4 items, you provided 1
Here, you have it. It says that -p needs 2 or 4 arguments, but you provided
only 1.
> I am not sure where I have to input the other 3 'p'. Please if could help me
> in figuring out where I am going wrong.
>
> Thank you for your time.
>
>
> Regards,
> Sulbha Choudhari
>
>
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