Hi all,
I'm Pierre Lindenbaum ; I work as a bioinformatician in Nantes/France.
It's the first time I'm invoking longranger mkfastq https://support.10xgenomics.com/genome-exome/software/pipelines/latest/using/mkfastq
this is my command:
module load longranger && \
longranger mkfastq \
--run="/sandbox/shares/u1087/novaseq/190517_A00797_0007_BHJTYVDMXX" \
--samplesheet="samplesheet.csv" \
--qc \
--output-dir="/sandbox/shares/u1087/lindenb/work/20190522.NOVASEQ" \
--jobmode=sge
(...)
longranger mkfastq (2.2.2)
(...)
[error] bcl2fastq exited with an error. You may have specified an invalid command-line option. See the full error here:
$ tail /sandbox/users/lindenbaum-p/notebook/2019/20190523.NOVASEQ/HJTYVDMXX/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0
<<illumina bcl2fastq help page...>>
Failed to parse the options: unrecognised option '--qc'
How can I fix this error ? I asked the support but I got still no answer. There must be something obvious ?
What version of bcl2fastq is getting used by
longranger mkfastq
?the ILMN bcl2fastq isn't bundled with longranger ? (I didn't install this software)
I think you have to provide it, but I've never seen a
--qc
option. As Genomax said, this is probably a documentation problem.Isn't the usual reason for "unrecognized option" a difference in versions? Any way you could verify if the version where you got the
--qc
option and the version loaded bymodule load
are compatible?@ramrs that was my question to devon: I don't know if the ILMN bcltofastq is embedded with longranger
No it is not. You need to make it available.
ok, but as far as I can see, my longranger is using the latest bcl2fastq 'v2.20.0.422' vs : https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf
That should be fine. That is what I use.