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.

…

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[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) This email originated from an EXTERNAL sender to CCHMC. Proceed with caution when replying, opening attachments, or clicking links in this message.

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.

…

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