I am trying to run the proname_refine script from the PRONAME pipeline using the provided Singularity container. However, the process consistently fails with the error: Fatal error: Unrecognized string on command line (0.9). According to the help menu, --clusterid 0.9 is a valid argument, but regardless of how I pass it (with or without quotes, or with =), I always get the same fatal error. I have tried running the command via Slurm scripts, directly with singularity exec, and even within an interactive Singularity shell session. I also inspected the script /opt/scripts/proname_refine inside the container and found that it uses getopts with single-letter flags instead of long-form options. For example, -a is used for clusterid, -c for inputpath, etc. When I switched to using the correct short-form flags (-a 0.9, -b 8, etc.), the command proceeded further and began clustering, but the documentation and error messages still refer to the long-form --clusterid, which is misleading. This has caused a lot of confusion and wasted effort. I would appreciate clarification on whether the long-form options are deprecated or incorrectly documented, and whether the script should support both formats or only the short ones.
Hello @ANTONIA_NACIFF_ROJAS,
The qiime2 team does not maintain the proname software. I'm sure the maintainers would appreciate the detailed detective work however, you can reach out to them on the software's GitHub page here.
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