Hello,
While running the read analysis section of the Qiime2 metagenomic analysis tutorial found here, I keep getting the following error:
`Plugin error from moshpit:
[Errno 2] No such file or directory: 'bracken'
Debug info has been saved to /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/qiime2-q2cli-err-z5tq_rr4.log`
and when I peak into the debugging file it looks like the bracken command cannot be found while the kraken one can.
qiime2-metagenome-2024.10) jrabasc@phpmb48 tests % cat /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/qiime2-q2cli-err-z5tq_rr4.log Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: bracken -d /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/qiime2/jrabasc/data/78cdef2b-953f-4e67-8e57-2ce95a0e6fc8/data -i /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/qiime2/jrabasc/data/ddbeb4dd-2c43-42d0-8a45-9a5c1836276e/data/ERR1428213.fastq.gz.report.txt -o /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/tmp283lzumn/ERR1428213.fastq.gz.bracken.output.txt -w /var/folders/bc/p3c9l5mj1qn06pfqwpnw35rw0000gq/T/qiime2/jrabasc/processes/55520-1734624741.919676@jrabasc/tmp/q2-OutPath-_hlcfzq7/ERR1428213.fastq.gz.report.txt -t 0 -r 100 -l S
Traceback (most recent call last): File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 530, in __call__ results = self._execute_action( File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 602, in _execute_action results = action(**arguments) File "<decorator-gen-698>", line 2, in estimate_bracken File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 299, in bound_callable outputs = self._callable_executor_( File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 570, in _callable_executor_ output_views = self._callable(**view_args) File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2_moshpit/kraken2/bracken.py", line 172, in estimate_bracken table, reports = _estimate_bracken( File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2_moshpit/kraken2/bracken.py", line 74, in _estimate_bracken bracken_table = _run_bracken_one_sample( File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2_moshpit/kraken2/bracken.py", line 46, in _run_bracken_one_sample run_command(cmd=cmd, verbose=True) File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/site-packages/q2_moshpit/_utils.py", line 44, in run_command subprocess.run(cmd, check=True, **kwargs) File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/subprocess.py", line 503, in run with Popen(*popenargs, **kwargs) as process: File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/subprocess.py", line 971, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "/Users/jrabasc/miniconda3/envs/qiime2-metagenome-2024.10/lib/python3.10/subprocess.py", line 1863, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'bracken'
Any guidance on how to fix this would be much appreciated! Thanks so much!
(we are going to update our documentation and the code to raise a more informative error, though).