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flexbar: Too many arguments!
Hey, here is my script:
**module load flexbar/3.5.0
DATA="/data/epifluidlab/lulu/hek293t/data"
mySample="Dmut2 Dmut3 Dyth1 Dyth2 Dyth3" for s in $mySample do
flexbar -r $DATA/${s}_1.fq.gz -p $DATA/${s}_2.fq.gz -aa Nextera –zip-output GZ –threads 16 -qf i1.8 -t /data/epifluidlab/lulu/hek293t/data/trim/${s}
done**
I got the error: flexbar: Too many arguments!
How could I fix it?
Thanks so much!
Best,
Lu
On 22/06/2023 13:17, lulumagic7 wrote:
Hey, here is my script:
**module load flexbar/3.5.0
DATA="/data/epifluidlab/lulu/hek293t/data"
mySample="Dmut2 Dmut3 Dyth1 Dyth2 Dyth3" for s in $mySample do
flexbar -r $DATA/${s}_1.fq.gz -p $DATA/${s}_2.fq.gz -aa Nextera –zip-output GZ –threads 16 -qf i1.8 -t /data/epifluidlab/lulu/hek293t/data/trim/${s}
done**
I got the error: flexbar: Too many arguments!
Hi, Lu.
Your long option "-threads" is incorrect: It should be "--threads"; same problem with your "-zip-output" option should be "--zip-output":
flexbar -r $DATA/${s}_1.fq.gz -p $DATA/${s}_2.fq.gz -aa Nextera --zip-output GZ --threads 16 -qf i1.8 -t /data/epifluidlab/lulu/hek293t/data/trim/${s}
HTH,
Tony.
-- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 @.***
Thanks so much!
From: Tony Travis @.*** Sent: Friday, June 23, 2023 11:51 AM To: seqan/flexbar @.> Cc: Lu, LU @.>; Author @.***> Subject: Re: [seqan/flexbar] flexbar: Too many arguments! (Issue #44)
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On 22/06/2023 13:17, lulumagic7 wrote:
Hey, here is my script:
**module load flexbar/3.5.0
DATA="/data/epifluidlab/lulu/hek293t/data"
mySample="Dmut2 Dmut3 Dyth1 Dyth2 Dyth3" for s in $mySample do
flexbar -r $DATA/${s}_1.fq.gz -p $DATA/${s}_2.fq.gz -aa Nextera –zip-output GZ –threads 16 -qf i1.8 -t /data/epifluidlab/lulu/hek293t/data/trim/${s}
done**
I got the error: flexbar: Too many arguments!
Hi, Lu.
Your long option "-threads" is incorrect: It should be "--threads":
flexbar -r $DATA/${s}_1.fq.gz -p $DATA/${s}_2.fq.gz -aa Nextera --zip-output GZ --threads 16 -qf i1.8 -t /data/epifluidlab/lulu/hek293t/data/trim/${s}
HTH,
Tony.
-- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 @.***mailto:***@***.***
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