Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

GCA_000001405.15_GRCh38_no_alt_analysis_set.fna is not a valid fasta file. #256

Open
gitterspec opened this issue Apr 20, 2023 · 1 comment
Open

GCA_000001405.15_GRCh38_no_alt_analysis_set.fna is not a valid fasta file. #256

gitterspec opened this issue Apr 20, 2023 · 1 comment

Comments

@gitterspec
Copy link

When using GCA_000001405.15_GRCh38_no_alt_analysis_set.fna as reference with -R flag.

The file is the extracted version of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

It is the reference that was used to align my samples.

In contrast, the official ftp://[email protected]/bundle/hg38/Homo_sapiens_assembly38.fasta.gz (also extracted) does not raise this error.
@mrmilhaven
Copy link

Hi,

I had this exact same issue. Changing the suffix from .fna > .fa fixed it for me.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@mrmilhaven @gitterspec