Hello
I'm trying to use cutadapt to trim my samples, however it gives me an error
trying to run:
qiime cutadapt trim-paired
--i-demultiplexed-sequences paired-end-demux.qza
--p-adapter-f CCTACGGGNGGCWGCAG
--p-adapter-r GACTACHVGGGTATCTAATCC \
--o-trimmed-sequences Trimmed.qza
--verbose
verbose gives me the following:
Running external command line application. This may print messages to stdout and/or stderr.
The commands to be run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: cutadapt --cores 1 --error-rate 0.1 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_9_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_21_L001_R2_001.fastq.gz --adapter CCTACGGGNGGCWGCAG -A GACTACHVGGGTATCTAATCC -A /tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_9_L001_R1_001.fastq.gz /tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_21_L001_R2_001.fastq.gz
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: --cores 1 --error-rate 0.1 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_9_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_21_L001_R2_001.fastq.gz --adapter CCTACGGGNGGCWGCAG -A GACTACHVGGGTATCTAATCC -A /tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_9_L001_R1_001.fastq.gz /tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_21_L001_R2_001.fastq.gz
Run "cutadapt --help" to see command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.
cutadapt: error: Adapter sequence is empty
Traceback (most recent call last):
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-249>", line 2, in trim_paired
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_cutadapt/_trim.py", line 189, in trim_paired
run_commands(cmds)
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_cutadapt/_trim.py", line 30, in run_commands
subprocess.run(cmd, check=True)
File "/home/vgirelli/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['cutadapt', '--cores', '1', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_9_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_21_L001_R2_001.fastq.gz', '--adapter', 'CCTACGGGNGGCWGCAG', '-A', 'GACTACHVGGGTATCTAATCC', '-A', ' ', '/tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_9_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_21_L001_R2_001.fastq.gz']' returned non-zero exit status 2.
Plugin error from cutadapt:
Command '['cutadapt', '--cores', '1', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_9_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-s31g0mlz/SRR18253047_21_L001_R2_001.fastq.gz', '--adapter', 'CCTACGGGNGGCWGCAG', '-A', 'GACTACHVGGGTATCTAATCC', '-A', ' ', '/tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_9_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-ikikjz6i/6c6e0b15-5471-4274-a339-ac7dfbaa2499/data/SRR18253047_21_L001_R2_001.fastq.gz']' returned non-zero exit status 2.
See above for debug info.
Any idea on what's causing it? I've looked a bit on the forum but similar errors seem to be issues fixed in newer versions