Program cannot find path for or to index file.

[mgb...@gmail.com]

Program cannot find path for or to index file.  Are index files designated as *.index?

 Multiple errors in IGV log file.  This time 42 after deleting and re-installing the IGV 2.4.10 program.  The original  IGV 2.4.10 produced 309 errors.   What is IGV snapshot?

I am using MacBook OS 10.13.5

What I did was open IGV --> File and select from File:  ran.bam.bai for BAM folder. This produced: Index is required, but no index found (see screenshot attached).

I expect and hope for a solution, what has happened is that after 3 weeks (including learning curve time), I have not made any progress. Now attaching the latest IGV log file.

[Helga Thorvaldsdottir]

Hi,

It looks like you are trying to view a bam file, but you loaded the index file instead of the bam file.

Bam files do indeed need a corresponding index file, but when you load the .bam file into IGV, it will look automatically for the corresponding index file in the same directory.

See http://software.broadinstitute.org/software/igv/BAM and http://software.broadinstitute.org/software/igv/AlignmentData for naming conventions and other info.

In your case you should load the "rna.bam" file and make sure the corresponding index file is in the same "BAM folder" and that it is named "rna.bam.bai" or "rna.bai".

IGV Snaphot is the latest development version of IGV from our nightly build. As described on the snapshot downloads page, it will contain features that have not been tested and is intended for advanced users only.

IGV will append to the log file every time you run the application. If you want to start with a fresh log file, you can remove or rename the old log file, and IGV will create a new one.

Helga

[Michael Bunnemeyer]

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Dear Helga,

Here are my results:

[James Robinson]

I think you are trying to load rna.bam.bai as the bam file.   Select rna.bam.     I think this was explained before but I did not get any response from you.

Could you make a screenshot of exactly that file you are selecting when you try to load the bam?  (It should be rna.bam).

On Mon, Jun 11, 2018 at 1:19 PM, Michael Bunnemeyer <mgb...@gmail.com> wrote:

On Jun 11, 2018, at 12:17 PM, Helga Thorvaldsdottir <he...@broadinstitute.org> wrote:

Hi,

It looks like you are trying to view a bam file, but you loaded the index file instead of the bam file.

Bam files do indeed need a corresponding index file, but when you load the .bam file into IGV, it will look automatically for the corresponding index file in the same directory.

See http://software.broadinstitute.org/software/igv/BAM and http://software.broadinstitute.org/software/igv/AlignmentData for naming conventions and other info.

In your case you should load the "rna.bam" file and make sure the corresponding index file is in the same "BAM folder" and that it is named "rna.bam.bai" or "rna.bai".

IGV Snaphot is the latest development version of IGV from our nightly build. As described on the snapshot downloads page, it will contain features that have not been tested and is intended for advanced users only.

IGV will append to the log file every time you run the application. If you want to start with a fresh log file, you can remove or rename the old log file, and IGV will create a new one.

Helga

On Sunday, June 10, 2018 at 2:15:00 PM UTC-4, mgb...@gmail.com wrote:

Program cannot find path for or to index file.  Are index files designated as *.index?

 Multiple errors in IGV log file.  This time 42 after deleting and re-installing the IGV 2.4.10 program.  The original  IGV 2.4.10 produced 309 errors.   What is IGV snapshot?

I am using MacBook OS 10.13.5

What I did was open IGV --> File and select from File:  ran.bam.bai for BAM folder. This produced: Index is required, but no index found (see screenshot attached).

I expect and hope for a solution, what has happened is that after 3 weeks (including learning curve time), I have not made any progress. Now attaching the latest IGV log file.

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Dear Helga,

Here are my results:

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[Michael Bunnemeyer]

<SS IGV  Bam Files - 2018-06-11 at 12.59.11 PM.png><Index is required but not found  with comment-  2018-06-07 at 11.24.33 AM.png>

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Thanks for responding!

I tried loading both files:  RNA.bam.bai   and RNA.bam.     Both produced the same error message.  Will attach screen shot.

[Michael Bunnemeyer]

On Jun 11, 2018, at 1:28 PM, James Robinson <jrob...@broadinstitute.org> wrote:

<SS IGV  Bam Files - 2018-06-11 at 12.59.11 PM.png><Index is required but not found  with comment-  2018-06-07 at 11.24.33 AM.png>

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[James Robinson]

Thanks for the additional information.   I will try to simulate this error with an external drive.   I do not know what is going on here.

BTW,  there is a lot of information in your log files,  that is by design,  but only a few errors  (all related to this one root problem).

[Helga Thorvaldsdottir]

I tried loading a bam file from an external drive with a path similar to yours on /Volumes with spaces in the pathname, but it worked just fine.

Can you try downloading this bam file and and corresponding index file, and see if you can load it into IGV.

Helga

[Michael Bunnemeyer]

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Hello Helga,

Thank you for trying, but unfortunately no success.  I downloaded your BRAF_C.bam.bai file.  This supposedly is an index file (because of the “bai” extension,  but the index is not found .  And the second line shows the path, also not recognized.  What is your assessment??

[Helga Thorvaldsdottir]

Hi,

You said you downloaded the BRAF_C.bam.bai file, but you don't mention whether you downloaded the BRAF_C.bam file.

Please try the following:

1) Make sure you've downloaded both files (the bam file and the index file) 

2) Put both files somewhere on your main disk (not on /Volumes/Seagate 6TB)

3) Start IGV

4) Select File > Load from File and use the file chooser to find where you put the files, select only the BRAF_C.bam file, and click Open

 

If that doesn't work - it's very strange. This is the most commonly viewed file type in IGV, and the BRAF_C files I've used as test files for a long time. I also tried changing the name of the bai file so it wasn't found, but entering it in that dialog that comes up for you fixes the problem and the data loads.

But if it doesn't work go ahead and:

1) send the igv.log file again

2) let us know how you installed IGV

Helga

[Michael Bunnemeyer]

Hello Helga,

The attachments show that both BRAF_C.bam and BRAF_C.bam.bai were downloaded (see attachment) - but only  BRAF_C.bam made it onto the Seagate external HB.  Please resend the BRAF_C.bam.bai (index file). Also note: “Safari can’t open the file.”  Any remedy for that?  What about screen sharing?

Best,

Michael

[Helga Thorvaldsdottir]

Michael,

Here are the links to the files again: the bam file and the index file.

If Safari tries to open them rather than download them, then don't click on the links, but rather right-click and pick "Download".

And then follow my instructions in the previous email. Note - I would like you try it from a local drive - don't put them on the /Volumes/Seagate 6TB/ drive.

If you need help downloading the files and running my suggested test, perhaps there's someone at your institution who can help. These are not IGV-specific issues you are running into now.

Helga

[Michael Bunnemeyer]

Hello Helga,

Thank you for resending the BRAF_C.bam.bai file.  I followed your instructions without any luck, or same dismal result.  I tried, while in IGV, to download  first BRAF_C.bam and then .bam.bai  and then in reverse.   I am not at any institution any longer.  Instead I have excellent Apple support, but they do not support programs like IGV,  although some have tried.  

Since this has been going on for three weeks, without any resolution in sight, I suggest trying something else, such as screen sharing. 

Look forwards to hearing from you.

Michael

(410-757-3368)

On Jun 12, 2018, at 11:55 AM, Helga Thorvaldsdottir <he...@broadinstitute.org> wrote:

index file