The bioBakery help forum

New version about PPANINI?

#1

Hello,
I install ppanini by conda,“conda install -c bioconda/label/cf201901 ppanini”
but the options are different in PPANINI tutorial,
the options on tutorial are

usage: ppanini [-h] -i INPUT_TABLE [-o OUTPUT_FOLDER] [--basename BASENAME]
               [--uniref2go UNIREF2GO] [--log-level LOG_LEVEL]
               [--tshld-abund TSHLD_ABUND] [--tshld-prev TSHLD_PREV]
               [--beta BETA] [--version]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_TABLE, --input_table INPUT_TABLE
                        REQUIRED: Gene abundance table with metadata
  -o OUTPUT_FOLDER, --output-folder OUTPUT_FOLDER
                        Folder containing results
  --basename BASENAME   BASENAME for all the output files
  --uniref2go UNIREF2GO
                        uniref to GO term mapping file
  --log-level LOG_LEVEL
                        Choices: [DEBUG, INFO, WARNING, ERROR, CRITICAL]
  --tshld-abund TSHLD_ABUND
                        [X] Percentile Cutoff for Abundance; Default=75th
  --tshld-prev TSHLD_PREV
                        Percentile cutoff for Prevalence
  --beta BETA           Beta parameter for weights on percentiles
  --version             prints the version

the options on tutorial from cf201901 ppanini are

  -h, --help            show this help message and exit
  -i INPUT_TABLE, --input_table INPUT_TABLE
                        REQUIRED: Gene abundance table with metadata
  -o OUTPUT_FOLDER, --output-folder OUTPUT_FOLDER
                        Folder containing results
  --gene-catalog GENE_CATALOG
                        GENE CATALOG
  --uc UC               UCLUST file containg centroids and clustered genes
  --usearch USEARCH     Path to USEARCH
  --vsearch VSEARCH     Path to VSEARCH
  --basename BASENAME   BASENAME for all the output files
  --log-level LOG_LEVEL
                        Choices: [DEBUG, INFO, WARNING, ERROR, CRITICAL]
  --threads THREADS     Number of threads
  --tshld-abund TSHLD_ABUND
                        [X] Percentile Cutoff for Abundance; Default=75th
  --tshld-prev TSHLD_PREV
                        Percentile cutoff for Prevalence
  --beta BETA           Beta parameter for weights on percentiles
  --bypass-clustering   Bypass clustering
  --version             prints the version

when I run “ppanini -i result/humann2/genfamilies_unstratified.tsv -o result/ppanini/” it give me an error:
At least one of --uc or --gene-catalog should be provided! Or use the flag --bypass-clustering to skip this step

Could please give me some advise about this options?

#2

I also have a question about --threads, when I use --threads 30,
this command does not seem to be multithreaded

 90756 ckzhu     20   0 13.535g 0.013t   7084 R 100.0  0.7  20:48.03 ppanini
#3

Hi there,

Thanks for using PPANINI!
The version you installed via conda seems still under-developing. We are working on further improvements.
Right now, PPANINI v0.7.3.1 is relatively stable. Could you please try to use this version instead (https://bitbucket.org/biobakery/ppanini/wiki/Home)? Use ‘pip install ppanini’ to install it. This version should have the same options described in PPANINI tutorial. You can use ‘ppanini_test’ to see if it’s installed correctly. Please let us know if it still doesn’t work for your data.

Thanks!
Yancong