Issue in adding test MAGs to database
Issue #32
closed
Hi Simon,
Thanks for this useful tool!
However, when I added the test MAGs to database, there was an issue:
Starting
[1] Get a list of genomes to import...
[2] Import information from GTDBtk trees...
Reading Wetland_MAGs_GTDB-tk_results/infer/gtdbtk.ar122.decorated.tree
Reading Wetland_MAGs_GTDB-tk_results/infer/gtdbtk.bac120.decorated.tree
[3] Load new host genomes in blast database...
[4] Get CRISPR arrays from new MAGs and add to database...
.....
[5] Add new genomes to WIsH database...
[6] Add new genomes to VHM database...
[7] Add new genomes to PHP database...
counting kmer ...
Preparing output file
done.
[8] Now build the new host genome metadata file...
Reading Wetland_MAGs_GTDB-tk_results/infer/gtdbtk.ar122.decorated.tree
Reading Wetland_MAGs_GTDB-tk_results/infer/gtdbtk.bac120.decorated.tree
We added 0 additional bacteria genomes and 0 additional archaea genomes
[9] All done
!#!#!#!#!#! WARNING --- SOME UNEXPECTED EVENTS HAPPENED -- WE LIST THEM BELOW, IT COULD BE NOTHING, BUT YOU SHOULD STILL DOUBLE-CHECK #!#!#!#!#!#!#
Note - we did not find a decorated file for the archaeal tree, so we did not use any data from a new archaeal genome
Note - we did not find a decorated file for the bacterial tree, so we did not use any data from a new bacterial genome
!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!#!#!
I am curious why this happened? My command is
iphop add_to_db --fna_dir Wetland_MAGs/ \
--gtdb_dir Wetland_MAGs_GTDB-tk_results/infer/ \
--out_dir Sept_2021_pub_w_Wetland_hosts \
--db_dir /data/virus.db/iphop_db/Sept_2021_pub_rw/
I checked the files in Wetland_MAGs_GTDB-tk_results/infer/
, there were archaeal and bacterial tree files.
By the way, I used the iphop with the standard database to predict hosts first, and it worked, no errors.
Thank you for your help.
Best
Zhongyi
Comments (4)
-
repo owner -
reporter It works! Thanks!
-
repo owner Perfect, thanks again for reporting !
-
repo owner - changed status to closed
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Hi Zhongyi,
Thanks for reporting this issue ! There was an inconsistency between the new code and the “Data_test_add_to_db.tar.gz” package. I uploaded a new version of the package that should work now, please try it out when you have a change (i.e. re-download the package via “wget https://bitbucket.org/srouxjgi/iphop/downloads/Data_test_add_to_db.tar.gz”, extract, and run “add_to_db” again).
Thanks again !
Best,
Simon