error when loading bam files

[xiaoyu liang]

Hello,

1. I'm using IGV 2.8.2 on Mac.

2. I'm trying to load bam file from a remote server(I've already mapped a network drive).

3. but I can't open the bam file and IGV gave me an error:

Error loading /Users/xiaoyuliang/Desktop/TRNlocal/mec8/A/MEC8AAligned.out_sorted.bam: An error occurred while accessing: /Users/xiaoyuliang/Desktop/TRNlocal/mec8/A/MEC8AAligned.out_sorted.bam
Error loading BAM file: htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Users/xiaoyuliang/Desktop/TRNlocal/mec8/A/MEC8AAligned.out_sorted.bam (Operation not permitted)

4. Can you help me out? is that something wrong when I map a network driver?

Best,

Xiaoyu

[xiaoyu liang]

BTW, everything works fine on IGV Web App, but not the IGV I downloaded on my Mac.

[James Robinson]

Are you running Catalina?  Catalina has some restrictions on what can be done with "Desktop" and "Documents" folders, maybe other but at least those 2.   Is there a way to map your network drive so that the path does not include "Desktop"?   This is a low level error. I don't know what could be done about it otherwise, but you might try a websearch on file permission problems with Catalina, Desktop, and mounted drives.

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[James Robinson]

Another workaround might be to download our Mac build from the "Snapshots" page and start it from the command line.  That might access the drives with different permissions.   I know it makes no sense to me either.

[xiaoyu liang]

Yea I'm running Catalina. Thanks for your prompt reply and pointing that out! I'll try a web search see what I can do on file permission problem~ I really appreciate that!

Best,

Xiaoyu

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[James Dipaola]

This happened to me also, I couldn’t open a bam through IGV tools on the desktop or downloads.  Fixed when I opened a bam, or any file, through File/Open in the IVG program.  This transmuted the access granted to IGV Tools.  Worked fine after doing this just once.  Hope it helps.

Sincerely,

Jed

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[James Robinson]

Thanks Jed, that's definitely worth a try.   

I think we are close to being able to "notarize" IGV, we had to wait on the Java JDK to be notarized first.   This will hopefully fix these Catalina quirks.

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[xiaoyu liang]

Thanks Jed! 

Best,

Xiaoyu

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[Robin J]

Hi, 

Sorry to post my problem under this thread. I'm having the exactly same problem. My system is upgraded into macOS Big Sur and my bam files are in Downloads. However, the problem is still there. 

How you solve the problem at last? I'm now using the web IGV to work.

Bests,

Jue

[James Robinson]

Hi Jue,

Please describe your problem in detail, what exactly are you doing and what is the error you are seeing?   Also, see the welcome message for this group for the type of information we need to diagnose a problem.

[Robin J]

Hi James, 

Thank you for the reply. 

1. tried IGV version 2.8 and 2.9. computer operating system is macOS Big Sur 

2. Like Xiaoyu, I use sshfs to remotely access my BAM from a server. I've checked the BAM and its index with Samtools view. 

3. my igv log file:

ERROR [2021-02-05T10:49:37,231] [IGV.java:1334]  Error loading track

org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam<br>Error loading BAM file: htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam (Operation not permitted)

at org.broad.igv.track.TrackLoader.load(TrackLoader.java:251) ~[igv.jar:?]

at org.broad.igv.ui.IGV.load(IGV.java:1399) ~[igv.jar:?]

at org.broad.igv.ui.IGV.loadResources(IGV.java:1331) [igv.jar:?]

at org.broad.igv.ui.IGV$4.run(IGV.java:474) [igv.jar:?]

at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) [igv.jar:?]

at java.util.concurrent.FutureTask.run(Unknown Source) [?:?]

at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]

at java.lang.Thread.run(Unknown Source) [?:?]

INFO [2021-02-05T10:49:37,234] [TrackLoader.java:122]  Loading resource, path /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam.bai

INFO [2021-02-05T10:49:37,243] [MessageUtils.java:76]  <html><b>ERROR:</b> Loading SAM/BAM index files are not supported:  /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam.bai<br>Load the SAM or BAM file directly. 

INFO [2021-02-05T10:49:42,881] [MessageUtils.java:76]  Error loading /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam: An error occurred while accessing:    /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam<br>Error loading BAM file: htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Users/jiangjue/Downloads/Gadi_bam/UP2142-B.final.bam (Operation not permitted)

INFO [2021-02-05T10:55:38,456] [ShutdownThread.java:47]  Shutting down

Comparing to your suggestion above,  my BAM is not in Desktop or Document, but under the folder of Dowloads. The web version IGV also works for me. 

Bests,

Jue

[James Robinson]

I don't understand, you said you are using sshfs to access a remote file, but then you said your BAM file is in your Downloads folder (as the log indicates). 

I do not have "Big Sur" to test with, but the Mac can be sensitive about files in certain folders.   You might try creating a folder directly under your user home directory and move the bam (and its index) there as a test.   But again I don't understand your reference to sshfs and remote files.

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[Robin J]

Hi,

Sorry that I didn't make myself clear. 

I use the tool `sshfs` to connect to a server and enable the local access of a BAM on that server without actually download it. In this way, I can open the BAM under the /Users/jiangjue/Downloads/Gadi_bam/ on my computer.  

Bests,

Jue

[James Robinson]

Ah, OK,  I know nothing about sshfs so I will not be much help.  The error message perhaps indicates that the application IGV does not have permission to access that file, as opposed to you as a user having permission.   Check the "Security and Privacy" system settings, under the "Privacy" tab, and see if IGV has permissions to access the Downloads folder.  If not grant it permission.   If that doesn't work I don't have a solution,  you might try loading a local file into IGV from Downloads to see if sshfs has anything to do with it.

Here's my "Privacy" settings, note that IGV has been granted access to Downloads and Desktop

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[Robin J]

Hi James,

Thank you for the solutions. I've checked my settings of privacy of files and folders in the system preference, but I don't see the IGV and its options. Also, the "+" button under the software lists does not allow me to add IGV or any other softwares into the list.

Bests,

Jue

[James Robinson]

Did you click the lock ("Click the lock to make changes")?

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[Robin J]

Yes, I’m now worry about the installation. 

For installation, I unzip the downloaded file, and then click on the IGV. You can see that it load the reference genome smoothly. 

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[James Robinson]

Do not use IGV 2.8.0,  it is well out of date.   I think we've established you can run IGV.   You will have to give it permissions to access your Downloads folder if you want to load files from there.   That is not an IGV question, it is a Mac OS question,  you probably need administrative privileges to do that, if you don't have them you will need to ask your administrator.

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[Robin J]

Hi James,

Thank you for helping me! I’ll look at the ways to allow the access. 

Bests,

Jue

On 5 Feb 2021, at 1:26 pm, James Robinson <jrob...@broadinstitute.org> wrote:

Do not use IGV 2.8.0,  it is well out of date.   I think we've established you can run IGV.   You will have to give it permissions to access your Downloads folder if you want to load files from there.   That is not an IGV question, it is a Mac OS question,  you probably need administrative privileges to do that, if you don't have them you will need to ask your administrator.

On Thu, Feb 4, 2021 at 6:18 PM Robin J <jueri...@gmail.com> wrote:

Yes, I’m now worry about the installation. 

For installation, I unzip the downloaded file, and then click on the IGV. You can see that it load the reference genome smoothly. 

<Screen Shot 2021-02-05 at 1.17.12 pm.png>

<Screen Shot 2021-02-05 at 1.18.21 pm.png>

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