Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: cutadapt --front file:/tmp/tmpceiha8pf --error-rate 0.1 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.1.fastq.gz --untrimmed-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/forward.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.2.fastq.gz --untrimmed-paired-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/reverse.fastq.gz /tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/forward.fastq.gz /tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/reverse.fastq.gz
This is cutadapt 3.2 with Python 3.6.13
Command line parameters: --front file:/tmp/tmpceiha8pf --error-rate 0.1 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.1.fastq.gz --untrimmed-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/forward.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.2.fastq.gz --untrimmed-paired-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/reverse.fastq.gz /tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/forward.fastq.gz /tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/reverse.fastq.gz
Traceback (most recent call last):
File "/home/jxu/miniconda3/envs/qiime2-2021.2/bin/cutadapt", line 10, in
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/cutadapt/main.py", line 845, in main_cli
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/cutadapt/main.py", line 899, in main
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/cutadapt/main.py", line 438, in open_output_files
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/cutadapt/main.py", line 504, in open_demultiplex_out
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/cutadapt/utils.py", line 167, in xopen
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/xopen/init.py", line 609, in xopen
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/xopen/init.py", line 519, in _open_gz
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/gzip.py", line 53, in open
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/gzip.py", line 163, in init
OSError: [Errno 24] Too many open files: '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/020.66154.48M.1.fastq.gz'
Traceback (most recent call last):
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in demux_paired
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_cutadapt/_demux.py", line 226, in demux_paired
error_rate, mux_fmt, batch_size, minimum_length)
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_cutadapt/_demux.py", line 177, in _demux
run_command(cmd)
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_cutadapt/_demux.py", line 37, in run_command
subprocess.run(cmd, check=True)
File "/home/jxu/miniconda3/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['cutadapt', '--front', 'file:/tmp/tmpceiha8pf', '--error-rate', '0.1', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.1.fastq.gz', '--untrimmed-output', '/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/forward.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.2.fastq.gz', '--untrimmed-paired-output', '/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/reverse.fastq.gz', '/tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/forward.fastq.gz', '/tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/reverse.fastq.gz']' returned non-zero exit status 1.
Plugin error from cutadapt:
Command '['cutadapt', '--front', 'file:/tmp/tmpceiha8pf', '--error-rate', '0.1', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.1.fastq.gz', '--untrimmed-output', '/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/forward.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-mbi4su5z/{name}.2.fastq.gz', '--untrimmed-paired-output', '/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-o5xiv04p/reverse.fastq.gz', '/tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/forward.fastq.gz', '/tmp/qiime2-archive-nyzr0wuv/5521c098-365e-442f-808d-1941dc0cba34/data/reverse.fastq.gz']' returned non-zero exit status 1.
See above for debug info.