cutadapt: error: unused arguments //not recognizing my sequences when using a loop?

Question

[Kirsten]

Hi all-- I'm fairly new at bioinformatics--I can usually find my way around errors (with the help of forums like these!)--but so far I have not been successful.

I'm running cutadapter through a Conda environment--and I have multiple primer sequences I am trying to remove. I've created a for loop for my primers here:

for i in *_R1_001.fastq.gz
do
  SAMPLE=$(echo ${i} | sed "s/_R1_001\.fastq\.gz//") 
  echo ${SAMPLE}_R1_001.fastq.gz ${SAMPLE}_R2_001.fastq.gz
cutadapt -g CTTGGTCATTTAGAGGAAGTAA -g CTTGGTCATTTAGAGGAAGTAA -g CTTGGTCATTTAGAGGAACTAA -g CCCGGTCATTTAGAGGAAGTAA -g CTAGGCTATTTAGAGGAAGTAA g- CTTAGTTATTTAGAGGAAGTAA -g CTACGTCATTTAGAGGAAGTAA -a GCATCGATGAAGAACGCAGC -a CCATCGATGAAGAACGCAGC -a GCATCGATGAAGAACGTAGC -a ACATCGATGAAGAACGCAGC -a ACATCGATGAAGAACACAGT -a GCAACGATGAAGAACGCAGC -a GCATCGATGAAGAACGC -G GCTGCGTTCTTCATCGATGC -G GCTGCGTTCTTCATCGATGG -G GCTACGTTCTTCATCGATGC -G GCTGCGTTCTTCATCGATGT -G ACTGTGTTCTTCATCGATGT -G GCTGCGTTCTTCATCGTTGC -G GCGTTCTTCATCGATGC -A TTACTTCCTCTAAATGACCAAG -A TTACTTCCTCTAAATGACCGAG -A TTAGTTCCTCTAAATGACCAAG -A TTACTTCCTCTAAATGACCGGG -A TTACTTCCTCTAAATAGCCTAG -A TTACTTCCTCTAAATAACTAAG -A TTACTTCCTCTAAATGACGTAG -n 2 --cores 4 -o ${SAMPLE}_R1_001.cut.fastq.gz -p ${SAMPLE}_R2_001.cut.fastq.gz ${SAMPLE}_R1_001.fastq.gz ${SAMPLE}_R2_001.fastq.gz
done

When I run

sh cutadapt.paired.used.sh

I get the following error over and over for all of my samples:

cutadapt: error: unrecognized arguments: CA18-REP1_S19_L001_R1_001.fastq.gz CA18-REP1_S19_L001_R2_001.fastq.gz
CA18-REP2_S20_L001_R1_001.fastq.gz CA18-REP2_S20_L001_R2_001.fastq.gz
Run "cutadapt --help" to see command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.

I've tried running the code on one sample (instead of all of them at once in a loop) and I get similar results:

cutadapt --pair-adapters -g CTTGGTCATTTAGAGGAAGTAA -g CTTGGTCATTTAGAGGAAGTAA -g CTTGGTCATTTAGAGGAACTAA -g CCCGGTCATTTAGAGGAAGTAA -g CTAGGCTATTTAGAGGAAGTAA g- CTTAGTTATTTAGAGGAAGTAA -g CTACGTCATTTAGAGGAAGTAA -a GCATCGATGAAGAACGCAGC -a CCATCGATGAAGAACGCAGC -a GCATCGATGAAGAACGTAGC -a ACATCGATGAAGAACGCAGC -a ACATCGATGAAGAACACAGT -a GCAACGATGAAGAACGCAGC -a GCATCGATGAAGAACGC -G GCTGCGTTCTTCATCGATGC -G GCTGCGTTCTTCATCGATGG -G GCTACGTTCTTCATCGATGC -G GCTGCGTTCTTCATCGATGT -G ACTGTGTTCTTCATCGATGT -G GCTGCGTTCTTCATCGTTGC -G GCGTTCTTCATCGATGC -A TTACTTCCTCTAAATGACCAAG -A TTACTTCCTCTAAATGACCGAG -A TTAGTTCCTCTAAATGACCAAG -A TTACTTCCTCTAAATGACCGGG -A TTACTTCCTCTAAATAGCCTAG -A TTACTTCCTCTAAATAACTAAG -A TTACTTCCTCTAAATGACGTAG -n 2 --cores 4 -o SK03_S36_L001_R1_001.cut.fastq.gz -p SK03_S36_L001_R2_001.cut.fastq.gz SK03_S36_L001_R1_001.fastq.gz SK03_S36_L001_R2_001.fastq.gz

Produces the following

cutadapt: error: unrecognized arguments: SK03_S36_L001_R1_001.fastq.gz SK03_S36_L001_R2_001.fastq.gz

I'm not sure what I'm doing wrong? Any help would be much appreciated!

Thnx

[swbarnes2]

For starters, are you sure that you can't use ambiguous codes instead of all those nearly identical -g's?

Answer 1

[cpad0112]

Code has a typo: g- CTTAGTTATTTAGAGGAAGTAA. Please fix that

[Kirsten]

That was definitely the problem. Thank you!