task_hasm() dies on missing ctgs

[flowers9]

Perhaps this is proper behavior, but in the deduping loop, if a ctg directory doesn't exist, the script exits:

for f incat ../reads/ctg_list ;do cd $WD/$f; fc_dedup_h_tigs.py $f; done

To get past this, I simply rewrote it as

for f in `cat ../reads/ctg_list`;do
if [ -d "$WD/$f" ]; then
cd $WD/$f
fc_dedup_h_tigs.py $f
fi
done

I'm not sure what a missing ctg directory implies - for example, if that's a critical error of some sort, and needs to be dealt with. If not, this patch a least allows the run to complete.

[jfass]

Check the "Possible MUMmer issue ..." issue ... doesn't answer your question, but there's other discussion of workarounds.

[yingzhang121]

I had the same issue. So I just manually created the directory for all the names in ctg_list. It seems this way can push fcunzip.py forward. However, I do suspect whether the missing contig will be correctly incorporated into the multiple all* output files.