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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/tmpwun0_xy0 --error-rate 0.1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.1.fastq.gz --untrimmed-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/forward.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.2.fastq.gz --untrimmed-paired-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/reverse.fastq.gz /tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/forward.fastq.gz /tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/reverse.fastq.gz
This is cutadapt 1.18 with Python 3.6.7
Command line parameters: --front file:/tmp/tmpwun0_xy0 --error-rate 0.1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.1.fastq.gz --untrimmed-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/forward.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.2.fastq.gz --untrimmed-paired-output /tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/reverse.fastq.gz /tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/forward.fastq.gz /tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/reverse.fastq.gz
Processing reads on 1 core in paired-end legacy mode …
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/xopen.py”, line 243, in _open_gz
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/xopen.py”, line 79, in init
OSError: [Errno 24] Too many open files: ‘/dev/null’
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.1/bin/cutadapt”, line 11, in
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/main.py”, line 798, in main
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/pipeline.py”, line 188, in run
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/pipeline.py”, line 329, in process_reads
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/filters.py”, line 299, in call
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/filters.py”, line 250, in call
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/seqio.py”, line 695, in open
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/seqio.py”, line 793, in _seqopen1
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/cutadapt/seqio.py”, line 468, in init
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/xopen.py”, line 294, in xopen
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/xopen.py”, line 245, in _open_gz
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/gzip.py”, line 53, in open
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/gzip.py”, line 163, in init
OSError: [Errno 24] Too many open files: ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/748.2.fastq.gz’
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-452>”, line 2, in demux_paired
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_cutadapt/_demux.py”, line 136, in demux_paired
return _demux(seqs, forward_barcodes, error_rate, untrimmed)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_cutadapt/_demux.py”, line 109, in _demux
run_command(cmd)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_cutadapt/_demux.py”, line 33, in run_command
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘cutadapt’, ‘–front’, ‘file:/tmp/tmpwun0_xy0’, ‘–error-rate’, ‘0.1’, ‘-o’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.1.fastq.gz’, ‘–untrimmed-output’, ‘/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/forward.fastq.gz’, ‘-p’, ‘/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-vjmx9ib5/{name}.2.fastq.gz’, ‘–untrimmed-paired-output’, ‘/tmp/q2-MultiplexedPairedEndBarcodeInSequenceDirFmt-qegwaj3r/reverse.fastq.gz’, ‘/tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/forward.fastq.gz’, ‘/tmp/qiime2-archive-70k6ct6n/65d2cb65-c12e-4337-9f64-5aad6ba7987d/data/reverse.fastq.gz’]’ returned non-zero exit status 1.