I’m also having this same error message, but only when I include in my database long sequences (> 200000 bp). You can find attached a file which I got an error message after using the command:
humann --input seqError2.fasta.txt --output /vol/volume2/outputTest
However, I have no error message if the long sequences is removed from the file, or if it is put at the beginning of the file (it is a bit strange that I can solve the problem by changing the position of the long sequence).
seqError2.fasta.txt (2.5 MB)