Closed mattbawn closed 4 years ago
Hi Matt,
I think there is here a mix of errors:
1) the first block from python script extract_metadata_from_gbff.py
actually belongs to task 00
but was not caught. It seems to come from a missing /db_xref="taxon:xxx"
field in one of the GenBank file. This field, which refers to the NCBI taxid, should be automatically added earlier in the automated annotation process - unless you provide your ownGenBank file and this field happens to be missing.
In commit db0409b, I changed the logging to provide more detail and made the pipeline to catch an error in extract_metadata_from_gbff.py
. Maybe you can re-run task 00
to sse what's wrong.
Ultimately, I could easily provide a default value for the taxid when not documented, but it is not super clean. please let me know.
2) Illegal instruction
is a dirty error message you don't want to see and means there is something wrong with your machine running mmseqs
, irrespective of the shell and pipeline around. Can you check mmseqs is correctly installed and up to date? it should be so through Homebrew. You can dig installation details with:
mmseqs -h | grep Version
which mmseqs
brew search mmseqs2
brew info mmseqs2
if it keeps throwing that kind of error, I suggest you compile the MMseqs program yourself from source (easy), available here: https://github.com/soedinglab/MMseqs2
I suggest you now use the Dockerfile to build a docker image, which should fix this kind of runtime problem, see #11 .
Hi Florent,
Task 0 now completes succesfully but I get the following:
However
/nbi/Research-Groups/IFR/Rob-Kingsley/R134_Pantagruel/database/logs/mmseqs/mmseqs-0-identicalprot-clusthash.log'
is empty.Thanks,
Matt