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 ?
•
written
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Pierre Lindenbaum
There is no --qc option for longranger mkfastq (at aleast with v.2.2.2).
I generally run with something like this:
module load longranger
longranger mkfastq --jobmode=slurm --maxjobs=24 --mempercore=16000 --run=/path_to/FCID --csv=./SampleSheet_10x.csv --output-dir=/path_to_FCID/mkfq
well, the manual says there is this option (?) https://support.10xgenomics.com/genome-exome/software/pipelines/latest/using/mkfastq
--qc (Optional) Calculate both sequencing and 10x-specific metrics, including per-sample barcode matching rate. Will not be performed unless this flag is specified.
you're right. same here.
well I see it in the longranger mkfastq online doc. I could run without --qc but I want to be sure that there is anything simple that could be fixed :-)
:-D
sorry , I'm new here.
I'm away from the lab. I'll test without --qc tomorrow.
Use a simple samplesheet like this with command I posted in answer.
Lane,Sample,Index
*,Sample1,SI-GA-A12
*,Sample2,SI-GA-C7
*,Sample3,SI-GA-C8
You will get folders for each sample at the end of the run.
If the same pool did not run in all lanes then you will add a lane number instead of *.
Does * actually work to specify "all lanes"? I just remove the Lane column completely in such cases.
Log in to answer this question.
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
--qcoption. 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
--qcoption and the version loaded bymodule loadare 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.