Trouble Building a Phylogeny with !

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Aug 17, 2016, 5:18:21 PM8/17/16
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I'm a new Qiime user and I'm attempting to build a phylogenetic tree based on a sample of eukaryotes (mainly algal). I'm using the Fungal ITs tutorial as a guide for my code but I'm getting a strange error when I run: -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$ -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/", line 453, in <module>


 File "/Library/Frameworks/Python.framework/Versions/2.7/bin/", line 432, in main


 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/", line 1071, in pick_subsampled_open_reference_otus


 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/", line 327, in align_and_tree


 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/qiime/workflow/", line 122, in call_commands_serially

   raise WorkflowError(msg)


*** ERROR RAISED DURING STEP: Align sequences

Command run was: -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



Traceback (most recent call last):

 File "/Library/Frameworks/Python.framework/Versions/2.7/bin/", line 211, in <module>


 File "/Library/Frameworks/Python.framework/Versions/2.7/bin/", 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/", line 266, in __call__


 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pynast/", 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/", line 707, in ipynast_seqs


 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skbio/alignment/", line 248, in __getitem__

   return self.get_seq(index)

 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skbio/alignment/", 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
align_seqs:template_fp silva_104/core_Silva_aligned.fasta
filter_alignment:suppress_lane_mask_filter True
filter_alignment:entropy_threshold 0.10

Jai Ram Rideout

Aug 17, 2016, 6:16:27 PM8/17/16
to Qiime 1 Forum

I've never seen this error before but I think the Silva 104 core alignment (silva_104/core_Silva_aligned.fasta) is causing issues due to the FASTA headers. The FASTA headers in that file contain whitespace and I think two different pieces of software are interpreting them in incompatible ways: one is (incorrectly) assuming the entire header is the sequence identifier, while the other is (correctly) parsing the FASTA header into a sequence identifier and description based on whitespace.

To work around this, you might try modifying core_Silva_aligned.fasta to not contain whitespace in the FASTA headers (make a backup of the original file first!). I'd truncate the header at the first occurrence of whitespace so that only the sequence identifier is retained. For example:

>AY191848.1.1408 1408 bp Ralstonia sp. 12F

would become:


You might also try newer versions of the Silva database; they shouldn't have this issue.

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