Closed gauravdiwan89 closed 1 year ago
Dear @gauravdiwan89, Thanks for trying out GenEra! I think there is more than one problem here. One can be attributed to a silly mistake in the GenEra code and the other might have something to do with the OS you are using.
In order for GenEra to rearrange the NCBI taxonomy, it downloads the correct information from the NCBI webpage using wget
to rearrange the ncbi_lineages
file generated by ncbitax2lin
. I think that your OS is having some problems while invoking wget
:
wget: /software/centos7/devel/anaconda/3/lib/libuuid.so.1: no version information available (required by wget)
Could you try running the following command on your machine?
wget -q "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock" && wc -l wwwtax.cgi\?mode\=Info\&id\=9606\&lvl\=3\&p\=has_linkout\&p\=blast_url\&p\=genome_blast\&lin\=f\&keep\=1\&srchmode\=1\&unlock | cut -d' ' -f1
The stdout of this command should print 456
.
Regarding the silly mistake in GenEra, I just created a patched version and uploaded it to GitHub. Please replace the executable genEra
in your machine with this new version and let me know if you still run into trouble.
Best, Josué.
Thanks a lot for the quick response!!
The wget
command did work with the exception that the stdout was 461
After replacing the source code for the genEra
executable, the program ran successfully!
Perfect, I'm glad that everything worked out!
Hello,
Really interesting software! I am just giving it a go and trying to determine the gene ages for the human proteome. I am using the fasta file for canonical human proteins from Uniprot and a Swissprot DIAMOND database for this purpose. I already also generated the ncbi_lineages file using
ncbitax2lin
. Thus the command that I used wasStep 1 runs correctly and so does a part of step 2 that creates the
tmp_column_*
files. However the run fails at the part where a rearranged ncbi_lineage file is created, specifically line 829 of genEraIt seems either the file is not created or there is an issue with opening it later. I do not know which one for sure as the program exits before I can know. The traceback is as follows
Can you please help me with this?
Thanks!