mash dist with -l: "ERROR: Did not find fasta records"

[snayfach]

I've encountered a possible bug in mash version 1.1.1 using the following command:
mash dist -p 5 sketch.msh -l genome_list.txt

where, sketch.msh is a sketch containing 129k genomes and genome_list.txt contains the path to those same genomes

That command produces the error:
ERROR: Did not find fasta records in "/path/to/fna/1281156.3.fna".

Which is weird because there ARE fasta records in that file. Further, this command works fine:

echo /path/to/fna/1281156.3.fna > genome_path.txt
mash dist -p 5 sketch.msh -l genome_path.txt

as does this one:
mash dist -p 5 sketch.msh /path/to/1281156.3.fna

I thought the issue might be related to the # of threads (-p 5). I tried re-running the first command without specifying the number of threads:
mash dist sketch.msh -l genome_list.txt

this seems to maybe be working? It was still running after about 30 minutes and didn't produce any error or output. The previous commands took only a minute or two to produce an error or output.

I've gotten around this issue for the time being by running mash dist over a loop, but a solution using a single mash command would be preferred. Any ideas?

[ondovb]

Looks like the same issue as #41. Fix is in master; release coming soon!

[ondovb]

Fixed in v2.0. Please reopen if issues persist.

[balags1]

This issue seems to persist in Mash v2.3, just noted.

[balags1]

Noted may be in error, my apologies, there was a file format issue.