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

[gitterspec]

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://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz (also extracted) does not raise this error.

[mrmilhaven]

Hi,

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