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…
Hi @Jingsi_Tang! Can you please provide the following info?
How did you generate the two files you’re trying to import? i.e.
Can you supply the first few lines of
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
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…
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.
This is my .biom.qzv file.table.qzv (680.4 KB)
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
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
Thank you for your response.
This is the result :
[email protected]:~/projects/2017_11_21_tang/clean_data$ wc -l reference-hit.seqs.fa
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep -v ‘^>’ reference-hit.seqs.fa | wc -l
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep ‘^>’ reference-hit.seqs.fa | wc -l
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep -v ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
[email protected]:~/projects/2017_11_21_tang/clean_data$ grep ‘^>’ reference-hit.seqs.fa | sort | uniq | wc -l
OK, out of ideas. Could you share the file with us? BTW, which version of qiime2 are you using?
This is the qiime 2017.10.0 version
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.
How to make the md5 checksum of my reference-hit.seqs.fa ? I am sorry I am not good at it…
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
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 for your reminding me. I think the new version will work for my data.
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