Bug in diamond only visible when using daa-meganizer


#1

Hi,

On latest commit diamond runs normally, when using MEGAN’s daa-meganizer I get the following error:

java.io.IOException: readNullTerminatedBytes(): failed (EOF)

which I assume has to do with how diamond finishes the daa file.

Error is hard to replicate because if daa-meganizer is executed again, no error is prompted and file meganizes normally. When visualizing in MEGAN, reads are overwhelmingly binned in high taxonomic nodes.

Already raised an issue in diamond’s github


#2

I’ve created a small database file and a small query if anybody wants to reproduce the error. Curiously, if you run daa-meganizer a second time on the failed file, no error happens and the file can be opened in MEGAN.

DB:
test.dmnd (354.5 KB)

Query:
test.fq (135.8 KB)

Bad daa:
failed.daa (54.4 KB)

Bad daa after running daa-meganizer for a first time:
failed2.daa (55.6 KB)


#3

Hi Julian,

this does not appear to be a Diamond problem, this looks like a meganizer problem… meganizer writes reference annotations to the DAA file and then reads them in again to do binning and that is when the problem occurs.
I have just spent a couple of hours trying to fix it, without luck… Did you only observe this on this one file?

Thanks
daniel


#4

Hi Daniel,

I observe this on every diamond run I make when using the latest commit.

The error does not happen when using previous versions of diamond. That’s why I think it can be a diamond issue.

best,
J