qiime worked only with --suppress_align_and_tree activated

[assa...@gmail.com]

Hello Qiime developers and users,

I was able to successfully run qiime default 16S pick_open_reference_otus.py function, only with the --suppress_align_and_tree option activated.
Without this option, the run terminates at one of its last stages (after producing the dir steps4_outs, and various OTU tables), and I'm getting the errors attached at the end of this message.

Qiime was executed using the default option:

pick_open_reference_otus.py -i $dirout1/combined_fasta/combined_seqs.fna -o $dirout1/$outLabel1/ \
                                    -p $dirout1/$outLabel1.clustering_params.txt \
                                        --parallel --jobs_to_start $threads1 \
                                            -s 0.1 -v --min_otu_size 10

thanks for your advice,
Assaf

error message:

Filter alignment
filter_alignment.py -o /data/home/x/y/z//pynast_aligned_seqs -i /data/home/x/y/z//pynast_aligned_seqs/rep_set_aligned.fasta
Build phylogenetic tree
make_phylogeny.py -i /data/home/x/y/z//pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o /data/home/x/y/z//rep_set.tre
[a@hv hive_logs]$ less error_p24_1348464.err
Traceback (most recent call last):
  File "/data/apps/python/2.7/bin/pick_open_reference_otus.py", line 453, in <module>
    main()
  File "/data/apps/python/2.7/bin/pick_open_reference_otus.py", line 432, in main
    minimum_failure_threshold=minimum_failure_threshold)
  File "/data/apps/python/2.7/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 1076, in pick_subsampled_open_reference_otus
    get_seq_ids_from_fasta_file(open(pynast_failures_fp, 'U')),
IOError: [Errno 2] No such file or directory: '/data/home/x/y/z//pynast_aligned_seqs/rep_set_failures.fasta'
[a@hv hive_logs]$ ls /data/home/x/y/z//pynast_aligned_seqs/rep_set_failures.fasta
ls: cannot access /data/home/x/y/z//pynast_aligned_seqs/rep_set_failures.fasta: No such file or directory
[a@hv hive_logs]$ ls /data/home/x/y/z/pynast_aligned_seqs/rep_set_failures.fasta
ls: cannot access /data/home/x/y/z/pynast_aligned_seqs/rep_set_failures.fasta: No such file or directory

[Jamie Morton]

Hi Assaf, 

Can you run the commands as follows, just to verify that your file paths are set properly. 

ls $dirout1/combined_fasta/combined_seqs.fna

ls $dirout1/$outLabel1/

ls $dirout1/$outLabel1.clustering_params.txt