My PI lied, what do I do?

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throwaway9010

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Why not offer to resubmit yourself and you do all the direct communication with the journal(s), with your PI remaining your sponsor? If you call the PI on the bluff, it will benefit no one. If you want the paper submitted, do it yourself (there has to be a 'first time' eventually).
 
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Something about this situation seems off to me. Are you certain that you and your PI have been on the same page about this manuscript? When you were ready to submit the last time, was the manuscript 100% ready to go out the door (formatting, references, title page, abstract, etc.)? I am trying to think of why a faculty member would have lied about this, and one thing that occurs to me is that it could have been a way to back out of a paper that he or she was not actually prepared to send out for some reason. That would be a cowardly thing to do but the thought comes to mind.

You're in a tricky situation but it's worth being assertive and trying to move things forward. Take ownership of the situation and try to get your PI to agree to some next steps. Make it easy for him or her to just say "OK." I would sidestep the matter of the fictional past journal submission and just look ahead.

I agree you should try to submit the paper yourself. Some online submissions systems are persnickety, which can be annoying, but it's not really difficult. Journal web sites have instructions (which few seem to read) that give you most of the information you will need. You can email the managing editor if you get stuck/lost. You can name your PI as the "corresponding author" even if you are the one to submit it. Ask to be cc'd on the journal correspondence as you'd like to learn from the process.

I like the tactic of saying "Unless there are major revisions necessary that I am unaware of, I would like to submit to Journal X by MM/DD," giving other authors a couple of weeks to write back with any further revisions. Just pushy enough to be effective!
 
Was any explanation offered for why the paper was withdrawn?

That seems the only difficult-to-explain red flag in all of this. I can think of few reasons for doing so unless they uncovered a major problem with the raw data or the analysis that raised some questions. My experience with the online journal systems is that they are wildly screwy so them not having a record of it being submitted or him having an account could be easily chalked up to technical glitches. I've had a couple odd issues myself even over the comparatively short window I've been submitting things as corresponding author.
 
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