Hi, I am trying to using cutadapt to trim the primers of the reads.
below is the script I ran.
qiime cutadapt trim-paired
--i-demultiplexed-sequences pair-end-demux.qza
--p-adapter-f GTTATTGTGATGTAGTTCCTG GTCGTTTTTGATCTGACAGG
--p-front-f CCTGTCAGATCAAAAACGAC CAGGAACTACATCACAATAAC
--p-adapter-r GTTATTGTGATGTAGTTCCTG GTCGTTTTTGATCTGACAGG
--p-front-r CCTGTCAGATCAAAAACGAC CAGGAACTACATCACAATAAC
--p-overlap 3
--p-error-rate 0.1
--p-match-read-wildcards
--p-match-adapter-wildcards
--p-minimum-length 1
--p-discard-untrimmed
--o-trimmed-sequences primer-trimmed-demux.qza
However, I got this error.
Plugin error from cutadapt:
Command '['cutadapt', '--cores', '1', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-q', '0,0', '--quality-base', '33', '-o', '/scratch/local/18008173/q2-CasavaOneEightSingleLanePerSampleDirFmt-4dvpif7_/cAE1-H_0_L001_R1_001.fastq.gz', '-p', '/scratch/local/18008173/q2-CasavaOneEightSingleLanePerSampleDirFmt-4dvpif7_/cAE1-H_9_L001_R2_001.fastq.gz', '--adapter', 'GTTATTGTGATGTAGTTCCTG', '--adapter', 'GTCGTTTTTGATCTGACAGG', '--front', 'CCTGTCAGATCAAAAACGAC', '--front', 'CAGGAACTACATCACAATAAC--p-adapter-r', '--front', 'GTTATTGTGATGTAGTTCCTG', '--front', 'GTCGTTTTTGATCTGACAGG', '-G', 'CCTGTCAGATCAAAAACGAC', '-G', 'CAGGAACTACATCACAATAAC--p-overlap', '-G', '3', '--match-read-wildcards', '--discard-untrimmed', '/scratch/local/18008173/qiime2/zjl1983/data/a979e63a-e044-4b35-bff0-1f8a16e452da/data/cAE1-H_0_L001_R1_001.fastq.gz', '/scratch/local/18008173/qiime2/zjl1983/data/a979e63a-e044-4b35-bff0-1f8a16e452da/data/cAE1-H_9_L001_R2_001.fastq.gz']' returned non-zero exit status 2.
Could anyone help me to find out what the problem is? And How to solve it?
Thank you!
Junli
