search

EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
34 stars 9 forks source link

empty/missing file eukcc.tsv #7

Open BiodivGenomic opened 4 years ago

BiodivGenomic commented 4 years ago

Hello, I'm trying to run EukCC on a small set of sequences, and for several of them, I got these messages.

substr outside of string at /home/hin175/soft/gmes_linux_64/get_sequence_from_GTF.pl line 172.
Use of uninitialized value in concatenation (.) or string at /home/hin175/soft/gmes_linux_64/get_sequence_from_GTF.pl line 172.
Use of uninitialized value in substr at /home/hin175/soft/gmes_linux_64/get_sequence_from_GTF.pl line 172.

For these sequences, the result file is either absent or empty (except the header line). Is there any way to fix it or to get more information from the error messages ? Thanks in advance !

openpaul commented 4 years ago

Hi,

There should be more error messages reported to you. It seems like there was an issue in the protein predictions or the phylogenetic placement. This can be caused by incomplete or very fragmented bins.

You can try adding the --debug flag to get more info.

You can check if the protein prediction failed by checking the output under workdir/gmes.