Hi all,
I'm working in R and trying to demultiplex some data using cutadapt
I have three files:
When I run the following code:
system2(cutadapt, args = c("-e 1 -g file:Y:/Vault/Tary_meta/Kim_2019/barcodes.fasta -o trimmed-Y:/Vault/Tary_meta/Kim_2019/cutadapt/Demulti/{name}.1.fastq.gz -p trimmed-Y:/Vault/Tary_meta/Kim_2019/cutadapt/Demulti/{name}.2.fastq.gz input.1.forward.fastq.gz input.2.reverse.fastq.gz --action=none"))
I first receive several warnings:
and the following error
Unfortunately I can't seem to find this error when searching through the cutadapt manual and past forum posts. Does anyone know what this error means and how I might resolve this?
I'm working in R and trying to demultiplex some data using cutadapt
I have three files:
barcodes.fastq.gz (which I have converted to Fasta format in R)
forward.fastq.gz
reverse.fastq.gz
forward.fastq.gz
reverse.fastq.gz
When I run the following code:
system2(cutadapt, args = c("-e 1 -g file:Y:/Vault/Tary_meta/Kim_2019/barcodes.fasta -o trimmed-Y:/Vault/Tary_meta/Kim_2019/cutadapt/Demulti/{name}.1.fastq.gz -p trimmed-Y:/Vault/Tary_meta/Kim_2019/cutadapt/Demulti/{name}.2.fastq.gz input.1.forward.fastq.gz input.2.reverse.fastq.gz --action=none"))
I first receive several warnings:
WARNING: Adapter 'CTAAGAGCCCGA' (regular 5') was specified multiple times! Please make sure that this is what you want.
and the following error
OSError: [Errno 22] Invalid argument: 'trimmed-Y:/Vault/Tary_meta/Kim_2019/cutadapt/Demulti/M03190:41:000000000-BBDRY:1:1101:15702:1567.1.fastq.gz
Unfortunately I can't seem to find this error when searching through the cutadapt manual and past forum posts. Does anyone know what this error means and how I might resolve this?
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