ERROR: Did not find fasta records

[HAugustijn]

I am using Mash with good results, but in about 1/10 times, I get the following error when sketching: ERROR: Did not find fasta records in "1234.fna".

If I take a look at the named fasta file, then it is a valid fasta file including a single sequence. If I rerun Mash on the same input files, Mash will run without an error.

I am using the following command: mash sketch -k 16 -p 10 -s 1000 -a /path/to/*.fna

[HAugustijn]

I noticed that this only occurs when multi threading, I never encounter this issue by using only one thread. In addition, when using multi threading (-p 10) the errors occur more frequently if my server becomes more crowded.

[jianshu93]

I have the same error when using multi-thread. It is really strange. What could be the reason?

THanks

Jianshu

[adriangeerre]

In my case, my run failed showing ERROR: Did not find fasta records in "input files". when running mash sketch. I investigate the last reported fasta file and it was not properly formated. After correcting it, it was solved.

Cheers

[HackenDirker]

Try running mash with GNU parallel. In my case, the native -p flag made the function call the wrong file as having a bad format. Running with GNU parallel made it much easier to find the bad fasta.