OSError: [Errno 18] Invalid cross-device link

[ZhuZhuoHSPH]

Hello~

Thank you for this awesome software. I'm trying to run lisa for some mouse genes and got the following error:
OSError: [Errno 18] Invalid cross-device link: '/tmp/tmpbipv10oa' -> '/home/eid/.conda/envs/conda-env-python3/lib/python3.7/site-packages/lisa/data/mm10/mm10_basic_2.1_RP_map.npz'
and
lisa.lisa_core.DownloadRequiredError: Data is malformed or incomplete, run "lisa download [species]" to redownload dataset.

I did lisa download mm10 and still got the same errors. However, I had none of the problems when testing using hg38. I wonder if you could help me to figure out what the problem could be. Thank you very much!

Best,
Zhu

[AllenWLynch]

I am deeply sorry for my late response. I have found the problem in the backend database for mm10 and corrected it, and I have tested the data download myself and things seem to be back on track. Please let me know if you further feedback. If you would like to try the mm10 test again, I am pushing an update next week that will make the downloading much faster and adds functionality for providing your own regions-of-interest for the test!

[ZhuZhuoHSPH]

Thanks Allen, I haven't used it again, but I'll report back once I do. Thanks!

[liulab-dfci]

I am releasing an update of LISA today or tomorrow which will include a new motif database based on JASPAR, a new Gene-TF targeting matrix output (https://github.com/liulab-dfci/lisa2/blob/master/docs/DataAnalysisGuide.md#Which-Genes-do-my-Factors-Target) and support for supplying your own ATAC/DNase peaks for factor enrichment. When you try your analysis again, I highly recommend upgrading to 2.2.1! Thanks again

[ChelseaCHENX]

I debugged via this post, for lisa/core/data_interface.py, line 70, in fetch_from_cistrome os.rename(filename, cls.get_dataset_path(species, window_size)), modify os.rename to shutil.move (and add import shutil to this file)

[AllenWLynch]

Thank you for pointing me to this issue. I was not aware that os.rename had this limitation. I will include this change in an update soon.

…

________________________________ From: Chelsea Chen ***@***.***> Sent: Wednesday, June 28, 2023 3:09 PM To: liulab-dfci/lisa2 ***@***.***> Cc: AllenWLynch ***@***.***>; Manual ***@***.***> Subject: Re: [liulab-dfci/lisa2] OSError: [Errno 18] Invalid cross-device link (Discussion #2) I debugged via this post<https://stackoverflow.com/questions/42392600/oserror-errno-18-invalid-cross-device-link>, for lisa/core/data_interface.py, line 70, in fetch_from_cistrome os.rename(filename, cls.get_dataset_path(species, window_size)), modify os.rename to shutil.move (and add import shutil to this file) — Reply to this email directly, view it on GitHub<#2 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AE43JPA7D3D7P6SP5HYKGB3XNSFPTANCNFSM4U6ARQYA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>