I’ve been having the same problem, so I’ve been following this thread to try to solve my problem. After following the script you suggested, I attempted to import my reference-hit.seqs.fa file again, and this time my error said: reference-hit.seqs.fa is not a(n) QIIME1DemuxFormat file
Earlier, the error was: not a(n) DNAFASTAFormat file
This is confusing to me, because I don’t know why it would require a single file to have 2 different formats. Is there a way to force the plugin to choose one format or the other?
I have the same problem with you… I am trying figure out it…
Hi @aeriel.belk, we need a bit more information before we can provide assistance:
- What version of QIIME 2 are you using?
- What were the exact commands you ran? Copy-and-paste please!
- What were the exact errors you observed? Copy-and-paste the results when run with
It sounds like you ran at least two different commands, judging by the errors you mention above, so if possible please provide both of those. Thanks!
I am using qiime2-2017.10. Here were my commands:
qiime tools import --input-path reference-hit.seqs.fa --output-path PMI3_Spring_rep-seqs.qza --type FeatureData[Sequence]
#Error: not a(n) DNAFASTAFormat file
wc -l reference-hit.seqs.fa
#output: 26714 reference-hit.seqs.fa
grep -v ‘^>’ reference-hit.seqs.fa | wc -l
grep ‘^>’ reference-hit.seqs.fa | wc -l
grep -v ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
grep ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
qiime tools import --input-path reference-hit.seqs.fa --output-path rep-seqs.qza --type SampleData[Sequence]
#Error: reference-hit.seqs.fa is not a(n) QIIME1DemuxFormat file
I’m realizing now as I typed this that I must have copied something wrong, because on my second try I have a different sample type. So, I just tried to run the import again using FeatureData[Sequence] on the data we changed with the grep commands, and I received the “not a(n) DNAFASTAFormat file” error again.
My best guess is that the program isn’t reading it as a .fasta file because the ID/sequence name is the same as the sequence itself. But if I just changed the sample ID that would probably mess things up downstream, right?
Great, thanks for the details @aeriel.belk!
First off, I recommend you see my post here, which recommends using
q2-deblur instead of
deblur produces data that needs a bit of massaging before it can be loaded into QIIME 2, that is where the advantage of
q2-deblur comes in - it does that clean-up for you!
Yep, I am noticing that too!
The data is unchanged —
grep is just a tool for searching within files, it is non-destructive. @antgonza was asking for @Jingsi_Tang to run some
grep commands to get a sense of the structure of the data, to make sure that there wasn’t anything too crazy happening in the fasta file.
I can’t say for sure, but ID-cleanup is one of the things happening in the
q2-deblur plugin, so if possible, I would recommend re-running your
deblur step in
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