Question: longranger mkfastq : "unrecognised option '--qc' "
0
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

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 ?

longranger mkfastq • 422 views
ADD COMMENTlink modified 12 months ago by genomax83k • written 12 months ago by Pierre Lindenbaum128k

What version of bcl2fastq is getting used by longranger mkfastq?

ADD REPLYlink written 12 months ago by Devon Ryan95k
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

the ILMN bcl2fastq isn't bundled with longranger ? (I didn't install this software)

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k

I think you have to provide it, but I've never seen a --qc option. As Genomax said, this is probably a documentation problem.

ADD REPLYlink written 12 months ago by Devon Ryan95k

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 by module load are compatible?

ADD REPLYlink written 12 months ago by RamRS27k

@ramrs that was my question to devon: I don't know if the ILMN bcltofastq is embedded with longranger

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k

No it is not. You need to make it available.

ADD REPLYlink written 12 months ago by genomax83k

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

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k
1

That should be fine. That is what I use.

ADD REPLYlink written 12 months ago by genomax83k
3
gravatar for genomax
12 months ago by
genomax83k
United States
genomax83k wrote:

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
ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax83k

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.
ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k
1

Not indicated in in-line help (longranger mkfastq -h).

ADD REPLYlink written 12 months ago by genomax83k

you're right. same here.

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k

--qc option is only available for cellranger.

ADD REPLYlink written 12 months ago by genomax83k

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 :-)

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k
1

You will get regular Illumina format demux report after running longranger.

ADD REPLYlink written 12 months ago by genomax83k

enter image description here

;-P

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint34k

:-D

sorry , I'm new here.

I'm away from the lab. I'll test without --qc tomorrow.

ADD REPLYlink written 12 months ago by Pierre Lindenbaum128k

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 *.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax83k

Does * actually work to specify "all lanes"? I just remove the Lane column completely in such cases.

ADD REPLYlink written 12 months ago by Devon Ryan95k

Yes * works.

ADD REPLYlink written 12 months ago by genomax83k
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