Question: Qiime parallel_align_seqs_pynast error Msg
0
gravatar for YOT
5.5 years ago by
YOT20
Canada
YOT20 wrote:

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

qiime php • 2.6k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 5.5 years ago by YOT20
1

Well, the formatdb command exited with status 3, which indicates an error. That's what it's complaining about. Try not suppressing output and see if you get something more informative. I'll note that this is also pretty off-topic and you might just want to find a PHP forum.

ADD REPLYlink written 5.5 years ago by Devon Ryan93k

try posting this on the qiime forum on google, they will get back to you within 24 hours
 

https://groups.google.com/forum/#!forum/qiime-forum

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by bio_boris20

Hey All,

Yes it is not  a PHP problem. It is a python script issue. A lot of people is facing different problems with parallel_align_seqs_pynast.

 

Thanks

ADD REPLYlink written 5.5 years ago by YOT20
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