Question: cutadapt error problem
0
gravatar for amitpande74
12 months ago by
amitpande740 wrote:

Hi,

I am trying to use cutadapt installed from conda. I am running this command :

cutadapt -a cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/barcodes.fasta  -o cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq input cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq

and it complains cutadapt: error: Too many parameters. Can someone kindly tell me what am I doing wrong here.

regards.

next-gen software error • 599 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by amitpande740

Start be getting rid of all of the cd instances in that command.

ADD REPLYlink written 12 months ago by Devon Ryan92k

Thanks for your replies.....kindly look here

I tried using it without cd but yet it complains about too many arguments.

cutadapt -a TCGCAGGACC -a CTCTGCAACC -a CCTAGGTACC -a GGATCAAACC -a GCAAGATACC -a ATGGAGAACC -a CTCGATGACC -a GCTCGAAACC -o /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq input /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq

The user manual says to put all the barcodes in one file with fastq header

cutadapt -a file:adapters.fasta -o output.fastq input.fastq

I tried this as well..

cutadapt -b /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/file:barcodes.fasta -o /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq.gz input /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq

So it says ... Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: Character '/' in adapter sequence '/MEDIA/MOLOY/LACIE/BBTRG/20180910_FMT-IBS-EXP1/TNZIPPED/FILE:BARCODES.FASTA' is not a valid IUPAC code. Use only characters XACGTURYSWKMBDHVN.

and curiously it reads the unzipped as TNZIPPED.

Kindly help.

ADD REPLYlink modified 12 months ago by Devon Ryan92k • written 12 months ago by amitpande740

Please use ADD COMMENT/ADD REPLY when responding to existing comments/posts to keep threads logically organized.

Error in this case is clear. It looks like you have a non-permissible character in your adapters.fasta file. Can you show the output of cat adapters.fasta command?

ADD REPLYlink written 12 months ago by genomax73k
>barcode01
CGCAGG
>barcode02
CTCTGCA
>barcode03
CCTAGGT
>barcode04
GGATCAA
>barcode05
GCAAGAT
>barcode06
ATGGAGA
>barcode07
CTCGATG
>barcode08
GCTCGAA
ADD REPLYlink modified 12 months ago by Devon Ryan92k • written 12 months ago by amitpande740

Assuming those are cell barcodes, you might want to use UMI tools instead.

ADD REPLYlink written 12 months ago by Devon Ryan92k

cutadapt -b /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/file:barcodes.fasta

-o /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq.gz input

/media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq

try to remove the word "input" from your command line, it seems not to reasonable for me.

ADD REPLYlink modified 12 months ago • written 12 months ago by piet1.7k
1
gravatar for genomax
12 months ago by
genomax73k
United States
genomax73k wrote:

cd is a separate unix command that is used for changing directories. It can't be included as a part of other program commands. When you provide full path/file names, like you have done, there is no need to change any directories. I think following should work.

cutadapt -a /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/barcodes.fasta  -o /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq
ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax73k
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