Hello folks,

I am running Qiime from a browser interface I developed.

When I run parallel_align_seqs_pynast it creates the results as expected.

I call from PHP in this way:

$result = $output_including_status = shell_exec("parallel_align_seqs_pynast.py -i ./HOT-ALOHA-otus.fasta -t ./core_set_aligned.fasta.imputed.txt -o ./result");
echo $result;

But it shows on browser the following error message

Traceback (most recent call last):
File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/parallel_align_seqs_pynast.py", line 106, in main()
File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/parallel_align_seqs_pynast.py", line 102, in main suppress_submit_jobs=False)
File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/parallel/util.py", line 136, in __call__ self._precommand_initiation(input_fp,output_dir,working_dir,params)
File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/parallel/align_seqs.py", line 29, in _precommand_initiation output_dir=get_qiime_temp_dir())
File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/formatdb.py", line 119, in build_blast_db_from_fasta_path app_result = fdb(fasta_path)
File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 251, in __call__ open(errfile).read()) 
cogent.app.util.ApplicationError: Unacceptable application exit status: 3 
Command: cd "/tmp//"; formatdb -l "core_set_aligned.fasta.imputed.txt.log" -o T -n "core_set_aligned.fasta.imputed.txt" -i "./core_set_aligned.fasta.imputed.txt" -p F > "/dev/null" 2> "/dev/null" StdOut: StdErr: 1

Does someone know what that means?

Thanks