Problem when reading in the second .hic file

[ReinhardUllmann]

Hello,
I have installed GENOVA on WSL2 (Ubuntu 22.04)
I can read in the the first .hic file without problems. However, when I try to read in the second file I get the following error:

Reading data...
Error in file(juicerPath, "rb") : cannot open the connection
In addition: Warning message:
In file(juicerPath, "rb") :
cannot open file '/mnt/d/HIC/12878_36_30.hic': Too many open files_

Any help is highly welcome
Reinhard

[teunbrand]

Hi there,

Does this happen too if you open a fresh R session?
AFAIK R has a limit on the number of connections (125, I think), but I've never seen that limit reached.

[ReinhardUllmann]

Hello, First of all many thanks for your quick reply! Yes, this also happens with a fresh R session. $MAT and $IDX look ok for the imported hic data, but it is impossible to save the workspace when quitting. Best wishes Reinhard Outlook für Android<https://aka.ms/ghei36> herunterladen

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________________________________ From: Teun van den Brand ***@***.***> Sent: Sunday, April 30, 2023 11:26:27 PM To: robinweide/GENOVA ***@***.***> Cc: ReinhardUllmann ***@***.***>; Author ***@***.***> Subject: Re: [robinweide/GENOVA] Problem when reading in the second .hic file (Issue #324) Hi there, Does this happen too if you open a fresh R session? AFAIK R has a limit on the number of connections (125, I think), but I've never seen that limit reached. — Reply to this email directly, view it on GitHub<#324 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AY2FZNMTU4KLC3B27H35AP3XD3KIHANCNFSM6AAAAAAXREKYTM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[teunbrand]

Strange, I don't know what causes this error. If you swap the order of loading files, does it also complain about the 2nd file, or does it complain about the 1st file?

[ReinhardUllmann]

I have tested different hic files in different orders. GENOVA reads in the first file with no error message, but refuses the import of a second one. I also tried to write the content of $MAT to csv for later import by the "original" import function. Write.csv failed for the same reason. I will test the installation on a different computer tommorow and will keep you updated. best wishes Reinhard Outlook für Android<https://aka.ms/ghei36> herunterladen

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________________________________ From: Teun van den Brand ***@***.***> Sent: Monday, May 1, 2023 2:48:03 PM To: robinweide/GENOVA ***@***.***> Cc: ReinhardUllmann ***@***.***>; Author ***@***.***> Subject: Re: [robinweide/GENOVA] Problem when reading in the second .hic file (Issue #324) Strange, I don't know what causes this error. If you swap the order of loading files, does it also complain about the 2nd file, or does it complain about the 1st file? — Reply to this email directly, view it on GitHub<#324 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AY2FZNKFUKIK76BRJNGRWPTXD6WIHANCNFSM6AAAAAAXREKYTM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ReinhardUllmann]

Hello, unfortunately, I was not able to solve the problem with the import of a second .hic file. My attempt to install the program on a second computer failed: Error: Failed to install 'unknown package' from GitHub: cannot open URL 'https://api.github.com/repos/robinweide/GENOVA/contents/DESCRIPTION?ref=HEAD' Yet, my guess is that this error has nothing to do with your program, but that this problem is caused by the proxy and firewall settings of our institution. I will keep you updated in case I find a solution. best wishes and many thanks Reinhard

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Reinhard Ullmann ***@***.***> hat am 01.05.2023 16:01 CEST geschrieben: I have tested different hic files in different orders. GENOVA reads in the first file with no error message, but refuses the import of a second one. I also tried to write the content of $MAT to csv for later import by the "original" import function. Write.csv failed for the same reason. I will test the installation on a different computer tommorow and will keep you updated. best wishes Reinhard Outlook für Android https://aka.ms/ghei36 herunterladen --------------------------------------------- From: Teun van den Brand ***@***.***> Sent: Monday, May 1, 2023 2:48:03 PM To: robinweide/GENOVA ***@***.***> Cc: ReinhardUllmann ***@***.***>; Author ***@***.***> Subject: Re: [robinweide/GENOVA] Problem when reading in the second .hic file (Issue #324) Strange, I don't know what causes this error. If you swap the order of loading files, does it also complain about the 2nd file, or does it complain about the 1st file? — Reply to this email directly, view it on GitHub #324 (comment), or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2FZNKFUKIK76BRJNGRWPTXD6WIHANCNFSM6AAAAAAXREKYTM. You are receiving this because you authored the thread.Message ID: ***@***.***>