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?