[BUG] ORF prediction silently skipped despite no --skipORF flag — confusing interaction with --include_ORF

[developer-wellfishtech]

Is there an existing issue for this?

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Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

Hi,

I opened a new bug, because, if I am correct, it may be worth removing the --skip_orf flag. So It is a different issues from #607

When running sqanti3_qc.py without --skipORF, ORF prediction is still skipped by default (log shows: Skipping ORF prediction because user requested it. All isoforms will be non-coding!, even though I never requested this). This happens consistently across fresh output directories, ruling out caching. After digging into sqanti3_config.yaml, I found include_ORF: false is the actual default, and the CLI flag --include_ORF must be explicitly passed to trigger TD2/Psauron. This is confusing given --skipORF still exists and reads as the expected opt-out mechanism for a default-on behavior (consistent with older GeneMarkS-T-era docs/behavior), when in practice ORF prediction is now default-off and requires opting in via a separate, not very discoverable flag. I am missing somethihg?

Code sample

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Error

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Anything else?

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[pabloati]

Hi, first of all, which version of SQANTI3 are you using?

Since release 5.5, the --skip_ORF flag was changed to --include_ORF and ORF prediction skipped by default due to the longer runtimes of TransDecoder2. This change has been documented in the wiki, and it can be seen in the help menu of sqanti3_qc.py:

ORF prediction:
  --include_ORF         Include ORF prediction.
  --orf_input ORF_INPUT
                        Input fasta to run ORF on. By default, ORF is run on genome-corrected fasta - this overrides it. If input is fusion (--is_fusion), this must be provided for ORF prediction.
  --psauron_threshold PSAURON_THRESHOLD
                        Threshold for P-Sauron ORF prediction (default: 0.5)..

My only concern is the cackt that you saw the option for --skip_ORF. Which release of sqanti3 are you using? You can see that via sqanti3_qc.py -v