'Error reading file null'

[Daniel Swan]

Has anyone else started to see this recently?  We interface to IGV via http to load BAMs and VCF files and jump to chromosomal locations.

Since last week we've noticed a lot of this error type popping up especially when populating the view with BAM files and zooming in on a region.  What is odd is that is seems quite sporadic, and affects various versions of IGV we've used when no previous problem exists.  Other people I know are experiencing this in different locations as well, but I've never had this issue prior to last week.

[Jacob Silterra]

Daniel,

Can you provide a bit more information:

What version of IGV are you running? (Should say in help -> about, or if using web start say so)
Can you provide a link to a problematic file and specify the location at which the error occurs?

-Jacob

On Thu, Aug 30, 2012 at 9:57 AM, Daniel Swan <dan....@gmail.com> wrote:

Has anyone else started to see this recently?  We interface to IGV via http to load BAMs and VCF files and jump to chromosomal locations.

Since last week we've noticed a lot of this error type popping up especially when populating the view with BAM files and zooming in on a region.  What is odd is that is seems quite sporadic, and affects various versions of IGV we've used when no previous problem exists.  Other people I know are experiencing this in different locations as well, but I've never had this issue prior to last week.

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Jacob Silterra
Software Engineer
Broad Institute

[Erik Larsson]

I'm having the same problem - on files I recently opened, with the same version of IGV. I have IGV installed locally...! Must be something silly on my side - did you ever figure this out?

Erik

[Erik Larsson]

Some more hints (console output):

ERROR [2012-09-26 13:00:04,947]  [IGVSequence.java:70] [pool-2-thread-6]  Error reading genome sequence from: http://www.broadinstitute.org/igvdata/annotations/seq/hg19/chr1.txt

java.net.SocketTimeoutException: connect timed out

Happens all the time now - running IGV both on my mac and linux (both v2017). Will update and see if it solves the problem...

[Daniel Swan]

No I didn't figure it out,  I'm still having intermittent issues with this issue and had also noted a lot of failed connection calls to the Broad servers, but I initially dismissed this as they seemed to predate the issues I was having in the logs.  

The reason I couldn't submit any additional information is that it is not related to any position or particular BAM file, such is the sporadic nature of it, but it normally manifests itself when I 'seek' to a position via the http call or zoom in, rather than on data load for vcf or bam files.

It does tend to resolve itself if you click through the dialogue and perhaps isn't as frequent as it was a couple of weeks ago - it is just odd. Nice to know it's not just me though..

Dan

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[Jim Robinson]

Hi,

Apologies for this,  we had a major power outage recently and have, apparently, still not recovered fully.   We're in the process of moving files to other servers but there are a lot of files,  so it is helpful to know what genome (sequence) you are accessing when you have this problem.   I note from Eric's response that hg19 files are affected,  what other assemblies?

I'm moving the hg19 files now,  it takes up to 24 hours to take affect, they are going to the Amazon "cloud" and there is a cache involved that takes time to clear.

-- Jim

[Daniel Swan]

Our problem specifically is with b37.

regards,

Dan

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--
Daniel Swan || dan.swan[at]gmail.com || http://eridanus.net/ ||
http://twitter.com/d_swan
"Reality is that which, when you stop believing in it, doesn't go away."
(Philip K. Dick - How to Build a Universe)

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