running a batch file: cannot open .bam file from shared network drive

[Brittany Greene]

IGV v2.3
OS: Linux Mint 15

I am trying to write a .txt batch file to automate taking snapshots of certain areas of interest. Before jumping into the automation, I wanted to make sure I could run a simple batch file to start a new session, open a file, specify a region, and save a snapshot. Below is the code I wrote:

new
load smb://172.17.50.54/synology_storage/Original_Data/NJLAGS_SEQ/wo231_disk1/LP6005170-DNA_A01/Assembly/genome/bam/LP6005170-DNA_A01.bam
goto chr1:113,144,120-113,164,120
snapshotDirectory /home/brzlab/Documents/IGV
snapshot test.png

When I ran this file, it executed all commands BUT did not open the .bam file. No error was displayed. I can open the file in the standard way- File>Load from File. Alternatively, I replaced the previous load statement with:

load /run/user/brzlab/gvfs/smb-share:server=172.17.50.54,share=synology_storage/Original_Data/NJLAGS_SEQ/wo231_disk1/LP6005170-DNA_A01/Assembly/genome/bam/LP6005170-DNA_A01.bam

This is the path that appears beside "resource" in the session.xml file when I load the file normally and save the session. It does not work either.
I think the problem lies in that the file is stored on a password-protected shared drive. The drive is mounted using samba.

Is there any way to load files from shared drives via a batch file? Is there something obviously wrong with what I wrote? Is there any resource you might suggest to help me figure this out?

Thanks a lot,
Brittany

[Jacob Silterra]

Hi Brittany,

When you load the file from a session (or File > Load) are you presented with a prompt for a password? Also, if you could send your igv.log file that would be very helpful.

-Jacob

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Broad Institute

[Brittany Greene]

Hi Jacob,

No, I am not prompted for a password when I open it via File > Load.
I'm not sure what an igv.log file is, but here is the batch file I ran and the session saved as an xml, if that helps. Let me know how to access the .log file and I will.

By the way, when I extracted a segment of the bam file and saved it locally, I had no problem accessing the local file.

Thanks,
Brittany

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[Jacob Silterra]

Hi Brittany,

Thanks for the extra info. The igv.log file is located at ~/igv/igv.log, it contains debugging information that may be helpful.

Thanks,

-Jacob

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[Brittany Greene]

Jacob-
Here's the .log file. Thanks for being so prompt!

Best,
Brittany

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[Jacob Silterra]

Hello,

I think that the second form (/run/user/brzlab/gvfs/smb-

share:server=172.17.50.54,share=synology_storage/Original_Data/NJLAGS_SEQ/wo231_disk1/LP6005170-DNA_A01/Assembly/genome/bam/LP6005170-DNA_A01.bam) would work, except that the batch script doesn't allow files to have commas in the name because one can also load comma separated lists of files. I've noted that is a bug, I'm thinking in an upcoming release commas will be allowed if the string is quoted. eg:

load "/run/user/brzlab/gvfs/smb-

share:server=172.17.50.54,share=synology_storage/Original_Data/NJLAGS_SEQ/wo231_disk1/LP6005170-DNA_A01/Assembly/genome/bam/LP6005170-DNA_A01.bam"

This is what we do with spaces. I'll let you know when that's implemented.

-Jacob

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[Brittany Greene]

Jacob,

Thanks a lot. Keep me posted. Any idea of when that would be implemented? 

If not soon, is there any possible work-around?

Thanks,

Brittany

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[Jacob Silterra]

Hi Brittany,

Since you can load from a session file, you could save a session file with the appropriate file in it and load the session file from the batch script instead.

A fix which doesn't involve IGV would be creating a symlink on your local machine to the network resource, and loading the symlink. As long as that file name doesn't have any commas in it I think that will work.

-Jacob

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[Brittany Greene]

Thanks a lot! Great idea, the symbolic links work

Have a great day

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[Brittany Greene]

Hi Jacob--

A few people in my lab are having problems running IGV, getting a message at start-up: "Warning: IGV is running with minimal available memory (516 mb)" We've had no trouble running the program with 10 gb's in the past on the same machines...

They just wanted to double check that IGV is aware of this issue. Thanks!

Best regards,

Brittany Greene

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[Jacob Silterra]

Hi Brittany,

How are they starting IGV? Double-clicking the jar directly will often incur this problem, one should start from the command line with -Xmx set (the builtin scripts use -Xmx2000m for 2GB of starting memory)

-Jacob

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[Brittany Greene]

They tried that, and when opening that way they get no error message but the memory usage caps out still at ~500. She said she also tried a bash open and via java...

Gillian is the colleague -- her email is sil...@dls.rutgers.edu. She just ran to class but she could give you more info about whats going wrong. 

Thanks a lot for your prompt repsonse,

Brittany

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