Fasta.files from deblur failed to import QIIME2 about generate rep-seqs.qza

Hi, I would like to import reference-hit.seqs.fa to QIIME2.
I can import reference-hit.biom successful.
but when I use qiime tools import --input-path reference-hit.seqs.fa --output-path rep-seqs.qza --type FeatureData[Sequence]. It reported the reference-hit.seq.fa is not a Featuredata[Sequence] format…
I dont know how to solve this problem…

Thanks

Hi @Jingsi_Tang! Can you please provide the following info?

  1. How did you generate the two files you’re trying to import? i.e. reference-hit.seqs.fa and reference-hit.biom

  2. Can you supply the first few lines of reference-hit.seqs.fa?

  3. Can you run qiime feature-table summarize on the .qza file you imported the .biom file into, and send me the output? That’ll be a single .qzv file.

Thanks!

Hi @jairideout Thank you for your response!!
1.How did you generate the two files you’re trying to import? i.e. reference-hit.seqs.fa and reference-hit.biom
my data are demultiplexed merged pair end data, and each sample have one fasta.file or fastq.file.
#deblur workflow --seqs-fp 01.CleanData --output-dir clean_data -t 250

2.Can you supply the first few lines of reference-hit.seqs.fa?
yes. the first line are the representative seqs as same as the second line…
For example, >atcg…
atcg…
>ggct…
ggct…

3.Can you run qiime feature-table summarize on the .qza file you imported the .biom file into, and send me the output? That’ll be a single .qzv file.
yes, I have the biom.qzv file, but i can not send you now, tomorrow when i go to the office, i will send it to you.

Thank you again.

Hi, @jairideout

This is my .biom.qzv file.table.qzv (680.4 KB)

Thanks.

Hi @Jingsi_Tang,

I have a couple of theories of what could be going on, could you send us the result of the commands below? Just copy/paste the lines below in the terminal, while you are in the same folder than your reference-hit.seqs.fa file.

wc -l 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

Thanks!

2 Likes

Hi, @antgonza
Thank you for your response.

This is the result :
[email protected]:~/projects/2017_11_21_tang/clean_data$ wc -l reference-hit.seqs.fa
7848 reference-hit.seqs.fa
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep -v ‘^>’ reference-hit.seqs.fa | wc -l
3924
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep ‘^>’ reference-hit.seqs.fa | wc -l
3924
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep -v ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
3924
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
3924

Thanks

OK, out of ideas. Could you share the file with us? BTW, which version of qiime2 are you using?

Hi, @antgonza

This is the qiime 2017.10.0 version

Thanks

At this point, the only way to figure the issue out is by taking a close look to your reference-hit.seqs.fa, could you share it? Also, to be sure, if you could send us the md5 checksum of that file, that will be great!

An off-topic reply has been split into a new topic: Problems Importing FASTA File

Please keep replies on-topic in the future.

Hi @antgonza

How to make the md5 checksum of my reference-hit.seqs.fa ? I am sorry I am not good at it…

Thanks…

Hi @Jingsi_Tang! I want to take a quick step back — it looks like you used deblur, instead of q2-deblur to generate the files you are attempting to import. It looks like q2-deblur does a little bit of cleanup and manipulation of the files it produces in order for them to be saved as QIIME 2 Artifacts. Would it be possible for you to rerun the denoising step using q2-deblur instead of deblur? I know that is a bit of a pain, but I suspect it will make things simpler for you in the end. If you are unfamiliar with q2-deblur, please see the Moving Pictures Tutorial, which dedicates a bit of the denoising section to q2-deblur. Thanks! :t_rex:

1 Like

Hi @thermokarst

I will try to use q2- deblur, but I have to wait for the qiime2 2017.11 version. Because my data is demuxed paired-end merged data ,each sample have one fasta.file/fastq.file.

Thank you

1 Like

Hi @Jingsi_Tang, the 2017.11 Release is now available! :heart: :tada: :t_rex: :1st_place_medal:

Hi, @thermokarst

Thank you for your reminding me. I think the new version will work for my data.

Thanks again.

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