DandD crashing in exact mode

[simolucaa]

Hi,
we are trying to use your tool on some bacterial datasets. So far the dashing mode is working fine.

However, when launching DandD with the following command:
./dandd tree --datadir ../../data/split_ecoli --tag ecoli --exact
the tool seems to crash. Attached, you can also find the log file containing the errors.

Any help is much appreciated.

ecoli_exact.log

[jessicabonnie]

Hi Marti,
It seems like KMC is struggling with at least one of the files and then choking on the incomplete output file when it tries to compute cardinality. So the kmc_pre and kmc_suf files exist but they aren't usable. I recommend testing those files using kmc itself to identify which one complains. Something like this:

unique_names=$(ls ../../data/split_ecoli/*.kmc_* | sed 's/\.[^.]*$//' | sort | uniq)
for name in $unique_names; do
    echo "Processing $name"
    kmc "${name}" <SOME COMMAND>
done

After you have found it, just delete those two kmc files and try again!