flexbar: Too many arguments!

[lulumagic7]

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

[tony-travis]

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 @.***

[lulumagic7]

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:@.>

— Reply to this email directly, view it on GitHubhttps://github.com/seqan/flexbar/issues/44#issuecomment-1604474174, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A3VHI3YCBNGYBYBYJHESQLLXMW3PPANCNFSM6AAAAAAZQDYICI. You are receiving this because you authored the thread.Message ID: @.**@.>>