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Bcl2fastq conversion

Hi,

I am trying to run bcl2fastq bash file in linux and I keep getting this error. How could I fix this.

"Failed to parse the options: too many positional options have been specified on the command line"

This is my bcl command

module load bcl2fastq2/2.20

bcl2fastq --runfolder-dir /home/projects/BCL_AH37YGBGXM -p 80 --output-dir /home/projects/fastq --sample-sheet /home/projects/llumina_sample sheet.csv --no-lane-splitting
fastq bc2fastq illumina bcl
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written by abiuma • abiuma

1 answer

You can't have spaces in file names (well not unless you go through some additional hoops). Your easiest bet is to change the samplesheet filename so the command changes from

/home/projects/llumina_sample sheet.csv

to

/home/projects/llumina_sample_sheet.csv

Using -p 80 is not recommended unless you have a very high performance storage system. 12-18 cores total are generally fine for demultiplexing. You should specify the threads explicitly like -r 6 -p 6 -w 6 (18 total in this example, see what then mean by looking at the in-line help).

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written by GenoMax GenoMax

Thank you! this helps.

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written by abiuma • abiuma

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