HI
I am using the command to cut amplicon primers from my sequences:
qiime cutadapt trim-paired
–i-demultiplexed-sequences SM_16S.qza
–p-cores 8
–p-front-f CCTACGGGNGGCWGCAG
–p-front-r GACTACHVGGGTATCTAATCC
–o-trimmed-sequences primer-trimmed-SM_16S.qza
–verbose
my job fails and gives the following out put
[8<----------] 00:00:01 35,585 reads @ 29.9 µs/read; 2.00 M reads/minuteTraceback (most recent call last):
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-461>”, line 2, in trim_paired
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_cutadapt/_trim.py”, line 189, in trim_paired
run_commands(cmds)
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_cutadapt/_trim.py”, line 30, in run_commands
subprocess.run(cmd, check=True)
File “/home/ubuntu/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘cutadapt’, ‘–cores’, ‘8’, ‘–error-rate’, ‘0.1’, ‘–times’, ‘1’, ‘–overlap’, ‘3’, ‘–minimum-length’, ‘1’, ‘-o’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-3bs4gjhm/134-ear-D7_S135_L001_R1_001.fastq.gz’, ‘-p’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-3bs4gjhm/134-ear-D7_S135_L001_R2_001.fastq.gz’, ‘–front’, ‘CCTACGGGNGGCWGCAG’, ‘-G’, ‘GACTACHVGGGTATCTAATCC’, ‘/tmp/qiime2-archive-xc0bgpmp/f8f3e18e-ab62-4705-9000-3b1d56570a3b/data/134-ear-D7_S135_L001_R1_001.fastq.gz’, ‘/tmp/qiime2-archive-xc0bgpmp/f8f3e18e-ab62-4705-9000-3b1d56570a3b/data/134-ear-D7_S135_L001_R2_001.fastq.gz’]’ returned non-zero exit status 1.
Plugin error from cutadapt:
Command ‘[‘cutadapt’, ‘–cores’, ‘8’, ‘–error-rate’, ‘0.1’, ‘–times’, ‘1’, ‘–overlap’, ‘3’, ‘–minimum-length’, ‘1’, ‘-o’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-3bs4gjhm/134-ear-D7_S135_L001_R1_001.fastq.gz’, ‘-p’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-3bs4gjhm/134-ear-D7_S135_L001_R2_001.fastq.gz’, ‘–front’, ‘CCTACGGGNGGCWGCAG’, ‘-G’, ‘GACTACHVGGGTATCTAATCC’, ‘/tmp/qiime2-archive-xc0bgpmp/f8f3e18e-ab62-4705-9000-3b1d56570a3b/data/134-ear-D7_S135_L001_R1_001.fastq.gz’, ‘/tmp/qiime2-archive-xc0bgpmp/f8f3e18e-ab62-4705-9000-3b1d56570a3b/data/134-ear-D7_S135_L001_R2_001.fastq.gz’]’ returned non-zero exit status 1.
See above for debug info.
I thought maybe my sequences did not import correctly so I imported it again but I am still getting the same output. I also validated my file and it says that the file is valid.
I do not understand the error.
Please help