Koen-vdl
commented
9 months ago Getting the same error as @maurkarr.
The issue is caused by the download_comments function which is used in updatedb.
You can apply a patch-up fix by commenting out line 138 of run_ngmaster.py
# download_comments(DBpath, db_list)
When the line is commented out updatedb won't be killed after failing download_comments and will continue to the next step make_mlst_db which is the final part of updatedb.
Notice this might be a bad idea when using the --comments option which is not enabled by default!
(ngmaster_env) koen_vdl@srvlxhpc1:~$ ngmaster --updatedb
WARNING: Updating DB will overwrite existing DB files.
Continue? [y/n]: y
Updating DB files ...
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngmast/porB.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngmast/tbpB.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngmast/ngmast.txt ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/penA.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/mtrR.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/porB.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/ponA.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/gyrA.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/parC.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/23S.tfa ... Done.
/home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/pubmlst/ngstar/ngstar.txt ... Done.
Adding: ngmast
Adding: ngstar
Building a new DB, current time: 02/21/2024 18:22:40
New DB name: /home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/blast/mlst.fa
New DB title: PubMLST
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/db/blast/mlst.fa
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 21312 sequences in 0.327632 seconds.
Created BLAST database for /home/koen_vdl/miniconda3/envs/ngmaster_env/lib/python3.9/site-packages/ngmaster/scripts/../db/blast/mlst.fa
Hello,
I am wanting to update the databases associated with ngmaSTAR, but keep receiving the following error once the NG-STAR alleles are meant to update:
WARNING: Updating DB will overwrite existing DB files. Updating DB files ... /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngmast/porB.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngmast/tbpB.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngmast/ngmast.txt ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/penA.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/mtrR.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/porB.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/ponA.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/gyrA.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/parC.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/23S.tfa ... Done. /usr/local/lib/python3.9/dist-packages/ngmaster-1.0.0-py3.9.egg/ngmaster/db/pubmlst/ngstar/ngstar.txt ... Done. Downloading NG-STAR information for individual alleles. This may take a while. ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
I am utilizing the --updatedb and --assumeyes flags.
Please let me know if I can provide more information.