cutadapt error problem

Question

[amitpande74]

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.

[Devon Ryan]

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

[amitpande74]

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.

[GenoMax]

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?

[amitpande74]

>barcode01
CGCAGG
>barcode02
CTCTGCA
>barcode03
CCTAGGT
>barcode04
GGATCAA
>barcode05
GCAAGAT
>barcode06
ATGGAGA
>barcode07
CTCGATG
>barcode08
GCTCGAA

[Devon Ryan]

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

[piet]

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.

Answer 1

[GenoMax]

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

Answer 2

[SwitchHitter]

In case someone is still having the same issue.

-a file:<adapter_file> seems to be working.

So the command would be

cutadapt -a file:/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