pick_open_reference_otus.py -i seqs.fna -r silva_104_rep_set.fasta -o otus_ft/ -p params.txt
The error message looks like this:
Mac-Pro:McManus_Gutter Karen$ pick_open_reference_otus.py -i seqs.fna -r silva_104_rep_set.fasta -o otus_ft/ -p params.txt -i seqs.fna -r silva_104_rep_set.fasta -o otus_ft/ -p params.txt
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pick_open_reference_otus.py", line 453, in <module>
main()
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pick_open_reference_otus.py", line 432, in main
minimum_failure_threshold=minimum_failure_threshold)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 1071, in pick_subsampled_open_reference_otus
status_update_callback=status_update_callback)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 327, in align_and_tree
close_logger_on_success=close_logger_on_success)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Align sequences
Command run was:
align_seqs.py -i otus_ft//rep_set.fna -o otus_ft//pynast_aligned_seqs --template_fp silva_104/core_Silva_aligned.fasta
Command returned exit status: 1
Stdout:
Stderr
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/align_seqs.py", line 211, in <module>
main()
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/align_seqs.py", line 194, in main
log_path=log_path, failure_path=failure_path)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/align_seqs.py", line 266, in __call__
temp_dir=get_qiime_temp_dir())
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pynast/util.py", line 812, in pynast_seqs
for seq, status in pynast_iterator:
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pynast/util.py", line 707, in ipynast_seqs
Sequence(seq=template_alignment[template_seq_id],moltype=DNA)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 248, in __getitem__
return self.get_seq(index)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 515, in get_seq
return self[self._id_to_index[id]]
KeyError: 'AY191848.1.1408 1408 bp Ralstonia sp. 12F'
I'm not sure what this error means and what I need to fix. My params.txt is as follows:
pick_otus:enable_rev_strand_match True
assign_taxonomy:assignment_method blast
assign_taxonomy:silva_104/Silva_taxa_mapping_104set_97_otus.txt
assign_taxonomy:silva_104/silva_104_rep_set.fasta
align_seqs:template_fp silva_104/core_Silva_aligned.fasta
filter_alignment:suppress_lane_mask_filter True
filter_alignment:entropy_threshold 0.10