Error: no population items seen in the annotations when using GAF file
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Hello and thanks for developing these tools.
I am trying to conduct an enrichment analysis and a using goatools within a conda environment hosted on a remote computing cluster.
I am just running the following line of code:
find_enrichment.py --indent $outliers $allgenes $gaf --ns=BP >shared_genes.go
where $outliers is the list of genes of interest in the study formatted like so:
ABCA7 ACBD6 ACP3 ADAM15 ADAMTS8 ADCY2 AFG3L2 AK9 ALLC AMN ANKS1B AP1B1 ARHGAP25 ARHGAP39 ARHGAP6
and $allgenes is the population list of genes (all genes present in my study species genome) like so:
A1CF A2M A2ML1 A4GALT AAAS AACS AADAC AAGAB AAK1 AAMDC AANAT AAR2 AARS1 AARS2 AASDH AASDHPPT
and $gaf is the goa.human.gaf file downloaded from the gene ontology website, which looks like:
UniProtKB W6CW81 PYDC5 enables GO:0003690 PMID:21873635 IBA MGI:MGI:101847|MGI:MGI:2686159|MGI:MGI:96429|PANTHER:PTN001385751|UniProtKB:O14862|UniProtKB:Q16666 F Pyrin domain-containing protein 5 PYDC5|POP3 protein taxon:9606 20211216 GO_Central UniProtKB W6CW81 PYDC5 enables GO:0005515 PMID:24531343 IPI UniProtKB:O14862|UniProtKB:Q16666 F Pyrin domain-containing protein 5 PYDC5|POP3 protein taxon:9606 20180903 UniProt UniProtKB W6CW81 PYDC5 enables GO:0005515 PMID:24531343 IPI UniProtKB:Q96P20 F Pyrin domain-containing protein 5 PYDC5|POP3 protein taxon:9606 20180903 UniProt UniProtKB W6CW81 PYDC5 involved_in GO:0002218 PMID:21873635 IBA MGI:MGI:2686159|PANTHER:PTN001385767|UniProtKB:O14862 P Pyrin domain-containing protein 5 PYDC5|POP3 protein taxon:9606 20190213 GO_Central
When I run this command, the error I receive is "**FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS"
From previous issues posted here, I thought it was a problem with the gene naming format, but when I manually search the GAF file to ensure that my gene symbols are present in that file I can confirm that they are present, so this does not appear to be the issue.
I should note that I am using the human gaf file as the reference genome I am using does not have a gaf, gene2go, or gapd file associated with it.
Any help navigating this error would be appreciated, for example do I somehow need to convert the gaf file to use it or is there some other action I can take?
Hello,
Thank you for your interest in GOA Tools and for your time to contact us. Thank you for the detailed description of the issue you are encountering and for trying to debug by looking at previous isues.
Can you include any log messages that you are seeing? This will help us get you running ASAP.
Regards,
DV Klopfenstein, PhD