Selective parameters are not passed

[sagar Utturkar]

Hi,

I am running Qiime with custom database and updating some of the parameters as:

pick_otus:enable_rev_strand_match True

assign_taxonomy:id_to_taxonomy_fp /AM_database/qiime_AM-master/maarjAM.id_to_taxonomy.5.txt

assign_taxonomy:reference_seqs_fp /AM_database/qiime_AM-master/maarjAM.5.fasta

parallel_align_seqs_pynast:template_fp /AM_database/qiime_AM-master/vt_types_mafft_aligned.fasta

I am getting the error as "rep_set_aligned.fasta" file is empty. This error is arising because the script "parallel_align_seqs_pynast.py" using default template file instead of one from the custom database. To overcome this, I included the appropriate file in parameter.txt.

parallel_align_seqs_pynast:template_fp /depot/bioinfo/data/Projects/1_Raw_Data/AM_database/qiime_AM-master/vt_types_mafft_aligned.fasta

In Qiime log file - I see that the parameter is read correctly but somehow it is not passed to the script. The script is running as below without specifying "--template_fp" parameter.

parallel_align_seqs_pynast.py -i openRef_ucl_rev_test//rep_set.fna -o openRef_ucl_rev_test//pynast_aligned_seqs -T --jobs_to_start 20

If I ran above command manually with "template_fp" parameter, then I get desired output. Is there anything wrong with my parameters file? Please suggest how to pass this parameter.

Thanks

Sagar

[Stefan Janssen]

can you try to also set

align_seqs:template_fp /AM_database/qiime_AM-master/vt_types_mafft_aligned.fasta

and see what happens?

[sagar Utturkar]

Thank you for the reply and suggestion. It worked as expected.

align_seqs:template_fp /AM_database/qiime_AM-master/vt_types_mafft_aligned.fasta

It was minor fix but was very tedious for inexperienced users. The issue is resolved.