fails at Busco

[jpwares]

Test run almost completes, but fails in BUSCO with:

WARNING The dataset you provided does not contain the file dataset.cfg, likely because it is an old version. Default species (fly, eukaryota) will be used as augustus species
ERROR Impossible to read /home/ubuntu/Oyster_River_Protocol/busco_dbs/eukaryota_odb9/
mv: cannot stat ‘run_test*’: No such file or directory
make: *** [/home/jpwares/Oyster_River_Protocol/sampleclone/reports/test.busco.done] Error 1

Any ideas? I did re-download eukaryota_odb9 and re-extract.

[macmanes]

Can you confirm for me that you have edited the config.ini file as per https://oyster-river-protocol.readthedocs.io/en/latest/aws_setup.html#edit-config-ini?

[jpwares]

At first I went OY! because I had done so the 1st time I tried to install ORP but seem to have missed the second. However I fixed that this morning, tried again no luck, tried again with a clean sample data directory, failed in same way.

WARNING The dataset you provided does not contain the file dataset.cfg, likely because it is an old version. Default species (fly, eukaryota) will be used as augustus species
ERROR Impossible to read $HOME/Oyster_River_Protocol/busco_dbs/eukaryota_odb9/
mv: cannot stat ‘run_test*’: No such file or directory
make: *** [/home/jpwares/Oyster_River_Protocol/sampleclone2/reports/test.busco.done] Error 1

BELOW my /software/config.ini file:
[busco]
lineage_path = $HOME/Oyster_River_Protocol/busco_dbs/eukaryota_odb9
force = True
quiet = False

[tblastn]
path = $HOME/Oyster_River_Protocol/software/anaconda/install/envs/orp_v2/bin/

[makeblastdb]
path = $HOME/Oyster_River_Protocol/software/anaconda/install/envs/orp_v2/bin/

[hmmsearch]
path = $HOME/Oyster_River_Protocol/software/anaconda/install/envs/orp_v2/bin/

thanks
John

[macmanes]

ok, few things to change and check..

in config.ini, change the $HOME/Oyster.. to /home/jpwares/Oyster... At one point BUSCO could not read variables.

Can you check to see that $HOME/Oyster_River_Protocol/busco_dbs/eukaryota_odb9 versus $HOME/Oyster_River_Protocol/sampleclone2/busco_dbs/eukaryota_odb9 actually exists?

[jpwares]

aw hell you caught me being lazy with my path. fixed. thank you very much, sorry for the novice error.