The output is missing

[dabaoniu]

Hi! I was trying to run padloc with

padloc --fna GCF_004358345.1.fna --outdir output_padloc --cpu 2

Then I get three output files: GCF_004358345.1.domtblout, GCF_004358345.1_prodigal.faa, and GCF_004358345.1_prodigal.gff. However, the two files _padloc.csv and _padloc.gff were not obtained, and I also got the warning:

Warning message:
One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
  dat <- vroom(...)
  problems(dat) 
Warning message:
One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
  dat <- vroom(...)
  problems(dat) 
Warning message:
In left_join(., hmm_meta, by = "hmm.name") :
  Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 11 of `x` matches multiple rows in `y`.
ℹ Row 1171 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.

I'd be really grateful for any insight!

[leightonpayne]

Hi @dabaoniu,

Can you please run the following to provide me with more information:

padloc --version; padloc --db-version; padloc --check-deps

Did you install PADLOC via conda or directly from GitHub? If via conda can you also run:

conda --version

Thanks!

[dabaoniu]

Hi @leightonpayne

Thank you for the quick response! This is the result after I ran the above command:

padloc --version; padloc --db-version; padloc --check-deps padloc v1.1.0 padloc-db v2.0.0 [11:02:14] >> R installed (4.3.1) [11:02:14] >> HMMER installed (3.3.2) [11:02:14] >> Prodigal installed (2.6.3) [11:02:15] >> R package 'tidyverse' installed (2.0.0) [11:02:15] >> R package 'yaml' installed (2.3.7) [11:02:16] >> R package 'getopt' installed (1.20.4)

conda --version conda 23.9.0

Cheers!

[leightonpayne]

Thanks!

Due to an update to the format of our defence system models, PADLOC-DB v2.0.0 is only compatible with PADLOC v2.0.0 (whereas your installation is v1.1.0),

I'd recommend installing PADLOC v2.0.0 from scratch:

# Remove your old PADLOC env (if applicable)
conda env remove -n padloc
# Install PADLOC v2.0.0
conda create -n padloc -c conda-forge -c bioconda -c padlocbio padloc=2.0.0

[dabaoniu]

The problem was solved. Thank you so much for your help!