I am having the same problem as @Pseudomonas84 importing my seqs.fna file into qiime2. I tried following your suggestion of including the source format parameter, so my command looked like this:
My file does not appear to have any lowercase letters, however I noticed that the ID line is the same as my sequence, and I’m wondering if that is the problem. Is there a way to fix that, or do you have another suggestion as to what the problem might be?
Hi @aeriel.belk,
your sequences are in standard fasta format, not a QIIME1DemuxFormat file. You can follow this tutorial example to import to a FeatureData[Sequence] file.
Hi @aeriel.belk, sorry to hear things aren’t going well . I just created a file (seqs.fna) using the output from the head command you listed above, and imported using the following command (this is what @Nicholas_Bokulich linked to above):
The sequences imported without raising an error. This is noteworthy, because the code that performs the validation of this format only reads the first 5 records to make its assessment — so even if your file has more records in it, the error you mentioned seeing above would’ve been caused by using just the first 5 records, which means I should have seen that error in my test (this isn’t entirely true - the sniffer could detect issues in other lines of the file).
Some requests:
Can you please double check that your import command is importing the file you want?
Can you please copy-and-paste the exact import command you are running?
Can you please copy-and-paste the complete error you are seeing?
Hi @aeriel.belk,
It looks like the issue is that a number of sequences contain lower-case characters. use the following to convert your file before importing: