Importing fasta sequence as SampleData

Hi, I generate some data . For the purpose of correcting my read, I had to transform my fastq into a fasta file. But now I have a hard time importing it as SampleData.

I try :

qiime tools import
–type SampleData[Sequences]
–input-path data.fasta
–output-path sequences.qza

I had the following error :

data.fasta is not a(n) QIIME1DemuxFormat file

My file look like a regular fasta :

000210e3-8a92-43ea-872b-fe1c4a01b009
TCGCCTACCGTGACGTGTTACCGTAGGAATGAATCCTTAGAGTTTGATCATGGCTCAGATTGAACGCTGGCAGCAGGCCTAACACATACAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTCGCTGACGAAGTGGCGGACAGGTGAGTAATGTCTGAAACTGCCTGATGGAGGGGATAACTACTGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACAGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGCGATAAGGTTAATAACCTTGTCGATTGACGTTACCCGCAGAAGAAGCACCAGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCAGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAGACTGACGCTCAGGTGCGAAAGCGTGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCGGAGCTAACGCGTTAAGTCGACCGCCTGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCAGAGAACTTTCAGAGATGGATTGGTGCCTTCAGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACGTGCTACAATGGCGCATACAAAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGAAGGATTCATTCCCACGGTAACACGTC
000409db-3bb2-4317-a811-3ac25761e90f
TGACGTGTTACCGTGGGAATGAATCCTTAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTAACACATACAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAGAGAGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCCCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGCGATAAGGTTAATAACCTTGTCGATTGACGTTACCCGCAGAAGCACCGGCTAACTCCATTGCCAGCAGCCGCGGTAATACGGAGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCAGAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACAGTAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCAGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGAAGGATTCATTCCCACGGTA

How can I import it ?

Thanks

1 Like

Hi @nbargues,

A fasta line should that with a > character.

>seq1
ATGCCG
>set2 
CATCAT

So, you’re missing that character.

Best,
Justine

1 Like

Hi @jwdebelius,

Sorry there is a typo in my previous post; there are obviously > character in each header’s sequence

Can you have a solution then ?

Cheers

After a close research on the forum , my issue is oddly similar to this one :

So there are not a specific solution to that topic either :confused:

I think based on that other post, @ebolyen may be a better person to ask.

Hi @nbargues - in order to import these SampleData[Sequences] you must ensure that the format follows this:

http://qiime.org/documentation/file_formats.html#demultiplexed-sequences

In particular, I notice that your reflines do not indicate the sample ID & the sequence ID, which violates the formatting assumptions of this format.

Take a peek at that link above and let us know how it goes.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.