Bcl2fastq conversion

Question

[abiuma]

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

Answer 1

[GenoMax]

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).

[abiuma]

Thank you! this helps.