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robinweide / GENOVA

GENome Organisation Visual Analytics
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Problem when reading in the second .hic file #324

Open ReinhardUllmann opened 1 year ago

ReinhardUllmann commented 1 year ago

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_3630.hic': Too many open files

Any help is highly welcome Reinhard

teunbrand commented 1 year ago

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 commented 1 year ago

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

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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 GitHubhttps://github.com/robinweide/GENOVA/issues/324#issuecomment-1529142693, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AY2FZNMTU4KLC3B27H35AP3XD3KIHANCNFSM6AAAAAAXREKYTM. You are receiving this because you authored the thread.Message ID: @.***>

teunbrand commented 1 year ago

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 commented 1 year ago

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

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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 GitHubhttps://github.com/robinweide/GENOVA/issues/324#issuecomment-1529677728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AY2FZNKFUKIK76BRJNGRWPTXD6WIHANCNFSM6AAAAAAXREKYTM. You are receiving this because you authored the thread.Message ID: @.***>

ReinhardUllmann commented 1 year ago

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

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 https://github.com/robinweide/GENOVA/issues/324#issuecomment-1529677728, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2FZNKFUKIK76BRJNGRWPTXD6WIHANCNFSM6AAAAAAXREKYTM. You are receiving this because you authored the thread.Message ID: @.***>