After a while the behavior has gotten worse. Now just moving the scroll bar with the mouse is causing the resizing behavior.
4) Minor annoyance: We used to be able to “File>Load from URL”, enter the URL, and press “Enter” to load the new URL. Now that the optional Index URL text box was added it is no longer possible to load the File URL by pressing enter. The “OK” button is mandatory.
1 & 2 seem related and are our most important issues. I can't tell if it is something on our server end, or in IGV. We didn't have these issues before the changes were made to our server, but we are able to eventually load our data through the server as it is currently configured. At the same time, our sysadmins are very security conscious and we don't have full knowledge of how they are routing requests.Again the major change to the url on our server was the change from HTTP to HTTPS, could that be causing our issues?
Thanks for any help!
Lisa
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synbio@genepool13:/global/dna/shared/synbio/MiSeqAnalysis/AYBBH/20160315_AYAHX/2073_1103381_AYAHX/bwa_dir$ ls -l
total 8448
-rw-r----- 1 synbio synbio 8599676 Mar 17 22:51 aligned_reads.bam
-rw-r----- 1 synbio synbio 96 Mar 17 22:51 aligned_reads.bam.bai
-rw-r----- 1 synbio synbio 139 Mar 17 22:51 call_summary.txt
-rw-r----- 1 synbio synbio 32 Mar 17 22:51 callable.bed
-rw-r----- 1 synbio synbio 7779 Mar 17 22:51 snps.gatk.vcf
-rw-r----- 1 synbio synbio 330 Mar 17 22:51 snps.gatk.vcf.idx
So that leads me to believe that when it is failing IGV just expects to find a .bed.idx or .bed.idx.gz file in the same directory with the same name as the bed.
-Lisa
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Your browser sent a request that this server could not understand.
the igv.log says this:
RROR [2016-03-25 15:26:46,295] [IGV.java:1462] Error loading session session : <br> https://synbioqc.jgi.doe.gov/analysis/P20160314/results/pool7.igv.xml<br>Bad Request <br> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>
org.broad.igv.exceptions.HttpResponseException: Bad Request <br> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:749)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614)
at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220)
at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214)
at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:111)
at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1420)
at org.broad.igv.ui.IGV$8.run(IGV.java:1397)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
INFO [2016-03-25 15:26:46,295] [MessageUtils.java:74] <html>Unexpected error: org.broad.igv.exceptions.HttpResponseException: Bad Request <br> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>
.<br>See igv.log for more details
Unfortunately I don't have access to the server logs.
The data did finally load after re-opening IGV a couple times. So it is weirdly intermittent. I assumed from the server logs that the problem was the 404's for the bed.idx, but it sounds like that should not be fatal. I will see if I can get the server logs for this particular request. Thank you for the prompt responses!
Lisa
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