port 60151 broken in igv 2.4.5, working in 2.3.92

[bwlang]

I do see a flash of a loading bar in 2.4 - but no authentication dialog like I get from 2.3.92

here are some tcpdump captures: not working (2.4.5, 2.4.0)

08:54:58.559611 IP6 localhost.54271 > localhost.60151: Flags [S], seq 1846293062, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153521384 ecr 0,sackOK,eol], length 0
08:54:58.559694 IP6 localhost.60151 > localhost.54271: Flags [S.], seq 1885080753, ack 1846293063, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153521384 ecr 153521384,sackOK,eol], length 0
08:54:58.559715 IP6 localhost.54271 > localhost.60151: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153521384 ecr 153521384], length 0
08:54:58.559730 IP6 localhost.60151 > localhost.54271: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153521384 ecr 153521384], length 0
08:54:58.560056 IP6 localhost.54271 > localhost.60151: Flags [P.], seq 1:1550, ack 1, win 12743, options [nop,nop,TS val 153521384 ecr 153521384], length 1549
08:54:58.560085 IP6 localhost.60151 > localhost.54271: Flags [.], ack 1550, win 12695, options [nop,nop,TS val 153521384 ecr 153521384], length 0
08:54:58.640953 IP6 localhost.60151 > localhost.54271: Flags [F.], seq 1, ack 1550, win 12695, options [nop,nop,TS val 153521462 ecr 153521384], length 0
08:54:58.640989 IP6 localhost.54271 > localhost.60151: Flags [.], ack 2, win 12743, options [nop,nop,TS val 153521462 ecr 153521462], length 0
08:54:58.641322 IP6 localhost.54271 > localhost.60151: Flags [F.], seq 1550, ack 2, win 12743, options [nop,nop,TS val 153521462 ecr 153521462], length 0
08:54:58.641357 IP6 localhost.60151 > localhost.54271: Flags [.], ack 1551, win 12695, options [nop,nop,TS val 153521462 ecr 153521462], length 0
08:54:58.641717 IP6 localhost.54273 > localhost.60151: Flags [S], seq 965144491, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153521462 ecr 0,sackOK,eol], length 0
08:54:58.641795 IP6 localhost.60151 > localhost.54273: Flags [S.], seq 2712664786, ack 965144492, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153521462 ecr 153521462,sackOK,eol], length 0
08:54:58.641815 IP6 localhost.54273 > localhost.60151: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153521462 ecr 153521462], length 0
08:54:58.641825 IP6 localhost.60151 > localhost.54273: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153521462 ecr 153521462], length 0
08:54:58.642162 IP6 localhost.54273 > localhost.60151: Flags [P.], seq 1:1550, ack 1, win 12743, options [nop,nop,TS val 153521463 ecr 153521462], length 1549
08:54:58.642185 IP6 localhost.60151 > localhost.54273: Flags [.], ack 1550, win 12695, options [nop,nop,TS val 153521463 ecr 153521463], length 0

working (2.3.92):

08:52:23.407689 IP6 localhost.54155 > localhost.60151: Flags [.], ack 1, win 12743, length 0
08:52:23.407726 IP6 localhost.60151 > localhost.54155: Flags [.], ack 2, win 12695, options [nop,nop,TS val 153367712 ecr 153297712], length 0
08:52:23.560330 IP6 localhost.60151 > localhost.54137: Flags [R.], seq 2460959415, ack 1104060248, win 12695, length 0
08:52:23.560369 IP6 localhost.60151 > localhost.54155: Flags [R.], seq 1, ack 2, win 12695, length 0
08:52:23.560383 IP6 localhost.60151 > localhost.54167: Flags [R.], seq 1, ack 1550, win 12695, length 0
08:52:23.561243 IP6 localhost.54218 > localhost.60151: Flags [S], seq 3030972753, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153367864 ecr 0,sackOK,eol], length 0
08:52:23.561260 IP6 localhost.60151 > localhost.54218: Flags [R.], seq 0, ack 3030972754, win 0, length 0
08:52:23.561678 IP6 localhost.54219 > localhost.60151: Flags [SEW], seq 2350730719, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153367865 ecr 0,sackOK,eol], length 0
08:52:23.561694 IP6 localhost.60151 > localhost.54219: Flags [R.], seq 0, ack 2350730720, win 0, length 0
08:52:23.562054 IP localhost.54220 > localhost.60151: Flags [SEW], seq 1476765717, win 65535, options [mss 16344,nop,wscale 5,nop,nop,TS val 153367865 ecr 0,sackOK,eol], length 0
08:52:23.562074 IP localhost.60151 > localhost.54220: Flags [R.], seq 0, ack 1476765718, win 0, length 0
08:52:53.612790 IP6 localhost.54231 > localhost.60151: Flags [SEW], seq 812385200, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153397647 ecr 0,sackOK,eol], length 0
08:52:53.612874 IP6 localhost.60151 > localhost.54231: Flags [S.], seq 3178539394, ack 812385201, win 65535, options [mss 16324,nop,wscale 5,nop,nop,TS val 153397647 ecr 153397647,sackOK,eol], length 0
08:52:53.612892 IP6 localhost.54231 > localhost.60151: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153397647 ecr 153397647], length 0
08:52:53.612907 IP6 localhost.60151 > localhost.54231: Flags [.], ack 1, win 12743, options [nop,nop,TS val 153397647 ecr 153397647], length 0
08:52:53.613531 IP6 localhost.54231 > localhost.60151: Flags [P.], seq 1:1550, ack 1, win 12743, options [nop,nop,TS val 153397647 ecr 153397647], length 1549
08:52:53.613558 IP6 localhost.60151 > localhost.54231: Flags [.], ack 1550, win 12695, options [nop,nop,TS val 153397647 ecr 153397647], length 0
08:53:00.634103 IP6 localhost.60151 > localhost.54231: Flags [P.], seq 1:59, ack 1550, win 12695, options [nop,nop,TS val 153404595 ecr 153397647], length 58
08:53:00.634140 IP6 localhost.54231 > localhost.60151: Flags [.], ack 59, win 12741, options [nop,nop,TS val 153404595 ecr 153404595], length 0
08:53:00.634384 IP6 localhost.60151 > localhost.54231: Flags [F.], seq 59, ack 1550, win 12695, options [nop,nop,TS val 153404595 ecr 153404595], length 0
08:53:00.634406 IP6 localhost.54231 > localhost.60151: Flags [.], ack 60, win 12741, options [nop,nop,TS val 153404595 ecr 153404595], length 0
08:53:00.634554 IP6 localhost.54231 > localhost.60151: Flags [F.], seq 1550, ack 60, win 12741, options [nop,nop,TS val 153404595 ecr 153404595], length 0
08:53:00.634586 IP6 localhost.60151 > localhost.54231: Flags [.], ack 1551, win 12695, options [nop,nop,TS val 153404595 ecr 153404595], length 0

[jrobinso]

Could you please describe the issue in more detail? Steps to reproduce would be helpful as well.

[bwlang]

Hi Jim:

When I attempt to use a "view in IGV" link from galaxy (a link to http://localhost:60151) I see no output (other than the brief flash of a loading dialog) in v2.4+ . When I run 2.3.92 first, I get a login dialog and IGV will fetch the appropriate ranges from galaxy.

Does that point you in the right direction? There used to be an easy way to get log output from IGV, but either I've forgotten how or it's not as obvious anymore (i'm using IGV on a Mac)

[jrobinso]

The port is definitely working in general. If you open the attached html (unzip it first) in a browser StaticLinkExamples.html.zip and select "Direct load with name" it should load a tdf (wiggle) track. You mentioned login, maybe that is the problem, I have no way to test that. The igv.log file should be in the "igv" folder under your home directory, that might have more information.

[bwlang]

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187]  GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default%2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam&genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1
ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)
    at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)
    at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)
    at org.broad.igv.batch.CommandListener.run(CommandListener.java:126)
    at java.lang.Thread.run(Thread.java:745)

[jrobinso]

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst notifications@github.com wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default%2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam&genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[bwlang]

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default%2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam&genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst notifications@github.com<mailto:notifications@github.com> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default%2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam&genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[jrobinso]

OK. It appears to be failing because IGV cannot find the genome with id "grch38_hs38d1_noalt". Obviously its finding it with 2.3.x. Is that genome in your Genome pulldown widget?

On Thu, Jan 11, 2018 at 10:40 AM, Brad Langhorst notifications@github.com wrote:

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com

%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default% 2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam& genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson <notifications@github.com< mailto:notifications@github.com>> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst <notifications@github.com< mailto:notifications@github.com>> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default% 2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam& genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+ data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[bwlang]

Yep it’s one of the system installed genomes (not a custom genome)

here’s some log output from 2.3.92 ( different genome)

INFO [2018-01-11 13:45:40,984] [GenomeManager.java:145] Loading genome: /Users/langhorst/igv/genomes/hg38.genome INFO [2018-01-11 13:45:42,709] [GenomeManager.java:192] Genome loaded. id= hg38 INFO [2018-01-11 13:45:42,798] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 13:45:57,947] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2F0f6bd4e5d8388eae%2Figv_bam%2Flocal_default%2F6681a9c5d6f68037%2Fdata%2Fgalaxy_0f6bd4e5d8388eae.bam&genome=?&merge=true&name=WGBS-2.aln.controls_bam HTTP/1.1 INFO [2018-01-11 13:45:58,015] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:45:58,016] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/0f6bd4e5d8388eae/igv_bam/local_default/6681a9c5d6f68037/data/galaxy_0f6bd4e5d8388eae.bam INFO [2018-01-11 13:46:04,197] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:15,297] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:52,261] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2Ff31ed9fbd847ed18%2Figv_bam%2Flocal_default%2F9879886ce52a8675%2Fdata%2Fgalaxy_f31ed9fbd847ed18.bam&genome=?&merge=true&name=WGBS-2.aln.md_bam HTTP/1.1 INFO [2018-01-11 13:46:52,263] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:46:52,263] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/f31ed9fbd847ed18/igv_bam/local_default/9879886ce52a8675/data/galaxy_f31ed9fbd847ed18.bam

Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:44 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

OK. It appears to be failing because IGV cannot find the genome with id "grch38_hs38d1_noalt". Obviously its finding it with 2.3.x. Is that genome in your Genome pulldown widget?

On Thu, Jan 11, 2018 at 10:40 AM, Brad Langhorst notifications@github.com<mailto:notifications@github.com> wrote:

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com<http://2Fgalaxy.neb.com

%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default% 2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam& genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst notifications@github.com<mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default% 2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam& genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+ data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[jrobinso]

Sorry if this should be obvious, but I don't know Galaxy at all. When you say "system installed", does that mean that a custom setting is used for IGV's "genome server url"? You can see this in the Advanced tab of the user preferences window.

Second question. If you launch IGV independent of Galaxy is that genome available for selection?

Third question, do you work out of the Ipswich office?

On Thu, Jan 11, 2018 at 10:51 AM, Brad Langhorst notifications@github.com wrote:

Yep it’s one of the system installed genomes (not a custom genome)

here’s some log output from 2.3.92 ( different genome)

INFO [2018-01-11 13:45:40,984] [GenomeManager.java:145] Loading genome: /Users/langhorst/igv/genomes/hg38.genome INFO [2018-01-11 13:45:42,709] [GenomeManager.java:192] Genome loaded. id= hg38 INFO [2018-01-11 13:45:42,798] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 13:45:57,947] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com

%2Fdisplay_application%2F0f6bd4e5d8388eae%2Figv_bam%2Flocal_default% 2F6681a9c5d6f68037%2Fdata%2Fgalaxy_0f6bd4e5d8388eae.bam& genome=?&merge=true&name=WGBS-2.aln.controls_bam HTTP/1.1 INFO [2018-01-11 13:45:58,015] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:45:58,016] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/0f6bd4e5d8388eae/ igv_bam/local_default/6681a9c5d6f68037/data/galaxy_0f6bd4e5d8388eae.bam INFO [2018-01-11 13:46:04,197] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:15,297] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:52,261] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2Ff31ed9fbd847ed18%2Figv_bam%2Flocal_default% 2F9879886ce52a8675%2Fdata%2Fgalaxy_f31ed9fbd847ed18.bam& genome=?&merge=true&name=WGBS-2.aln.md_bam HTTP/1.1 INFO [2018-01-11 13:46:52,263] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:46:52,263] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/f31ed9fbd847ed18/ igv_bam/local_default/9879886ce52a8675/data/galaxy_f31ed9fbd847ed18.bam

Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:44 PM, Jim Robinson <notifications@github.com< mailto:notifications@github.com>> wrote:

OK. It appears to be failing because IGV cannot find the genome with id "grch38_hs38d1_noalt". Obviously its finding it with 2.3.x. Is that genome in your Genome pulldown widget?

On Thu, Jan 11, 2018 at 10:40 AM, Brad Langhorst <notifications@github.com mailto:notifications@github.com> wrote:

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com

%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default% 2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam& genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson <notifications@github.com< mailto:notifications@github.com>< mailto:notifications@github.com>> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst < notifications@github.commailto:notifications@github.com< mailto:notifications@github.com>> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com %2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default% 2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam& genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+ data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[jrobinso]

It makes sense to me, BTW, that the IGV 2.3.92 output works. The genome there is "hg38", which is known to IGV, the genome from the 2.4 output "grch38_hs38d1_noalt", is not.

On Thu, Jan 11, 2018 at 11:00 AM, James Robinson < jrobinso@broadinstitute.org> wrote:

Sorry if this should be obvious, but I don't know Galaxy at all. When you say "system installed", does that mean that a custom setting is used for IGV's "genome server url"? You can see this in the Advanced tab of the user preferences window.

Second question. If you launch IGV independent of Galaxy is that genome available for selection?

Third question, do you work out of the Ipswich office?

On Thu, Jan 11, 2018 at 10:51 AM, Brad Langhorst <notifications@github.com

wrote:

Yep it’s one of the system installed genomes (not a custom genome)

here’s some log output from 2.3.92 ( different genome)

INFO [2018-01-11 13:45:40,984] [GenomeManager.java:145] Loading genome: /Users/langhorst/igv/genomes/hg38.genome INFO [2018-01-11 13:45:42,709] [GenomeManager.java:192] Genome loaded. id= hg38 INFO [2018-01-11 13:45:42,798] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 13:45:57,947] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com

%2Fdisplay_application%2F0f6bd4e5d8388eae%2Figv_bam%2Floc aldefault%2F6681a9c5d6f68037%2Fdata%2Fgalaxy 0f6bd4e5d8388eae.bam&genome=?&merge=true&name=WGBS-2.aln.controls_bam HTTP/1.1 INFO [2018-01-11 13:45:58,015] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:45:58,016] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/0f6bd4e5d8388eae/i gv_bam/local_default/6681a9c5d6f68037/data/galaxy_0f6bd4e5d8388eae.bam INFO [2018-01-11 13:46:04,197] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:15,297] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:52,261] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2Ff31ed9fbd847ed18%2Figv_bam%2Floc aldefault%2F9879886ce52a8675%2Fdata%2Fgalaxy f31ed9fbd847ed18.bam&genome=?&merge=true&name=WGBS-2.aln.md_bam HTTP/1.1 INFO [2018-01-11 13:46:52,263] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:46:52,263] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/f31ed9fbd847ed18/i gv_bam/local_default/9879886ce52a8675/data/galaxy_f31ed9fbd847ed18.bam

Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:44 PM, Jim Robinson <notifications@github.com<mail to:notifications@github.com>> wrote:

OK. It appears to be failing because IGV cannot find the genome with id "grch38_hs38d1_noalt". Obviously its finding it with 2.3.x. Is that genome in your Genome pulldown widget?

On Thu, Jan 11, 2018 at 10:40 AM, Brad Langhorst < notifications@github.commailto:notifications@github.com> wrote:

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com

%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default% 2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam& genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson <notifications@github.com mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst < notifications@github.commailto:notifications@github.com< mailto:notifications@github.com>> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com %2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default% 2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam& genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+ data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[bwlang]

I tested on the same files originally.. I just did not have them handy for the log checks. As you mentioned I think the lack of a dialog may be the root of this issue… without it, any request for a resource in galaxy would fail - maybe leading to the null pointer exception.

Brad

On Jan 11, 2018, at 7:39 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

It makes sense to me, BTW, that the IGV 2.3.92 output works. The genome there is "hg38", which is known to IGV, the genome from the 2.4 output "grch38_hs38d1_noalt", is not.

On Thu, Jan 11, 2018 at 11:00 AM, James Robinson < jrobinso@broadinstitute.orgmailto:jrobinso@broadinstitute.org> wrote:

Sorry if this should be obvious, but I don't know Galaxy at all. When you say "system installed", does that mean that a custom setting is used for IGV's "genome server url"? You can see this in the Advanced tab of the user preferences window.

Second question. If you launch IGV independent of Galaxy is that genome available for selection?

Third question, do you work out of the Ipswich office?

On Thu, Jan 11, 2018 at 10:51 AM, Brad Langhorst notifications@github.com<mailto:notifications@github.com

wrote:

Yep it’s one of the system installed genomes (not a custom genome)

here’s some log output from 2.3.92 ( different genome)

INFO [2018-01-11 13:45:40,984] [GenomeManager.java:145] Loading genome: /Users/langhorst/igv/genomes/hg38.genome INFO [2018-01-11 13:45:42,709] [GenomeManager.java:192] Genome loaded. id= hg38 INFO [2018-01-11 13:45:42,798] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 13:45:57,947] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com<http://2Fgalaxy.neb.com

%2Fdisplay_application%2F0f6bd4e5d8388eae%2Figv_bam%2Floc aldefault%2F6681a9c5d6f68037%2Fdata%2Fgalaxy 0f6bd4e5d8388eae.bam&genome=?&merge=true&name=WGBS-2.aln.controls_bam HTTP/1.1 INFO [2018-01-11 13:45:58,015] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:45:58,016] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/0f6bd4e5d8388eae/i gv_bam/local_default/6681a9c5d6f68037/data/galaxy_0f6bd4e5d8388eae.bam INFO [2018-01-11 13:46:04,197] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:15,297] [HttpUtils.java:856] Range-byte request succeeded INFO [2018-01-11 13:46:52,261] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2Ff31ed9fbd847ed18%2Figv_bam%2Floc aldefault%2F9879886ce52a8675%2Fdata%2Fgalaxy f31ed9fbd847ed18.bam&genome=?&merge=true&name=WGBS-2.aln.md_bam HTTP/1.1 INFO [2018-01-11 13:46:52,263] [IGV.java:1701] Loading 1 resources. INFO [2018-01-11 13:46:52,263] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/f31ed9fbd847ed18/i gv_bam/local_default/9879886ce52a8675/data/galaxy_f31ed9fbd847ed18.bam

Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:44 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com<mail to:notifications@github.commailto:notifications@github.com>> wrote:

OK. It appears to be failing because IGV cannot find the genome with id "grch38_hs38d1_noalt". Obviously its finding it with 2.3.x. Is that genome in your Genome pulldown widget?

On Thu, Jan 11, 2018 at 10:40 AM, Brad Langhorst < notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

That was 2.4.0

here’s a 2.4.5 log

INFO [2018-01-11 13:39:07,043] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com

%2Fdisplay_application%2F73797ec427624ebc%2Figv_bam%2Flocal_default% 2F5c079101d2907698%2Fdata%2Fgalaxy_73797ec427624ebc.bam& genome=?&merge=true&name=Lot39AB-2_1-34.4ug-2.aln.md_bam HTTP/1.1 ERROR [2018-01-11 13:39:07,208] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

Brad

— Brad Langhorst, Ph.D. Development Scientist New England Biolabs

On Jan 11, 2018, at 1:37 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

OK, that's helpful, but what version of IGV is this log from exactly? I'm having a hard time lining up the line numbers with the current code.

On Thu, Jan 11, 2018 at 6:14 AM, Brad Langhorst < notifications@github.commailto:notifications@github.commailto:notifications@github.com< mailto:notifications@github.com>> wrote:

ah - log file helps

INFO [2018-01-11 09:13:37,099] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com< http://2Fgalaxy.neb.com %2Fdisplay_application%2F67cbe889dbbdf4c3%2Figv_bam%2Flocal_default% 2F2d7bdf7419d9b789%2Fdata%2Fgalaxy_67cbe889dbbdf4c3.bam& genome=grch38_hs38d1_noalt&merge=true&name=Bowtie2+on+ data+1481+and+data+1480%3A+aligned+reads+%28sorted+BAM%29.dups_marked HTTP/1.1 ERROR [2018-01-11 09:13:37,261] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:176)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:745)

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[jrobinso]

I don't recall a reference to a dialog, in what context?

The 2.4.0 genome referenced is not an IGV genome (grch38_hs38d1_noalt). You indicated that this genome is in your IGV pulldown menu, correct? That is, if you start IGV independent of Galaxy it is available for selection in this pulldown

​

On Thu, Jan 11, 2018 at 4:48 PM, Brad Langhorst notifications@github.com wrote:

I tested on the same files originally.. I just did not have them handy for the log checks. As you mentioned I think the lack of a dialog may be the root of this issue… without it, any request for a resource in galaxy would fail - maybe leading to the null pointer exception.

Brad

[jrobinso]

I'm asking for IGV 2.4 specifically, sorry the screenshot is 2.3.59 but the genome pulldown is the same.

On Thu, Jan 11, 2018 at 5:14 PM, James Robinson <jrobinso@broadinstitute.org

wrote:

I don't recall a reference to a dialog, in what context?

The 2.4.0 genome referenced is not an IGV genome (grch38_hs38d1_noalt). You indicated that this genome is in your IGV pulldown menu, correct? That is, if you start IGV independent of Galaxy it is available for selection in this pulldown

​

On Thu, Jan 11, 2018 at 4:48 PM, Brad Langhorst notifications@github.com wrote:

I tested on the same files originally.. I just did not have them handy for the log checks. As you mentioned I think the lack of a dialog may be the root of this issue… without it, any request for a resource in galaxy would fail - maybe leading to the null pointer exception.

Brad

[bwlang]

I've just captured fresh logs to eliminate the genome as a factor...

both are triggered to load data by visiting this URL: http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151]  Startup  IGV Version 2.3.97 (157)07/10/2017 10:52 PM
INFO [2018-01-11 20:14:41,120] [Main.java:152]  Java 1.8.0_151
INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72]  Fetching user directory...
INFO [2018-01-11 20:14:41,274] [Main.java:153]  Default User Directory: /Users/langhorst
INFO [2018-01-11 20:14:41,274] [Main.java:154]  OS: Mac OS X
INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613]  Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome
INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89]  Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp
INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134]  Download complete.  Total bytes downloaded = 6418326
INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163]  Loading genome: /Users/langhorst/igv/genomes/hg19.genome
INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210]  Genome loaded.  id= hg19
INFO [2018-01-11 20:14:54,212] [CommandListener.java:106]  Listening on port 60151
INFO [2018-01-11 20:16:43,060] [CommandListener.java:167]  GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1
INFO [2018-01-11 20:16:43,070] [IGV.java:1684]  Loading 1 resources.
INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126]  Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam
INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838]  Range-byte request succeeded
INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838]  Range-byte request succeeded
INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51]  Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51]  Shutting down
INFO [2018-01-11 20:25:36,944] [Main.java:154]  Startup  IGV Version snapshot 01/09/2018 06:52 PM
INFO [2018-01-11 20:25:36,944] [Main.java:155]  Java 1.8.0_151
INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76]  Fetching user directory...
INFO [2018-01-11 20:25:37,019] [Main.java:156]  Default User Directory: /Users/langhorst
INFO [2018-01-11 20:25:37,019] [Main.java:157]  OS: Mac OS X
INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182]  Loading genome: /Users/langhorst/igv/genomes/hg19.genome
INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271]  Genome loaded.  id= hg19
INFO [2018-01-11 20:25:50,373] [CommandListener.java:120]  Listening on port 60151
INFO [2018-01-11 20:26:02,501] [CommandListener.java:187]  GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1
ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)
    at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)
    at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)
    at org.broad.igv.batch.CommandListener.run(CommandListener.java:126)
    at java.lang.Thread.run(Thread.java:748)

[jrobinso]

Hmm, somehow we're not communicating. If you start IGV stand-alone, no Galaxy, is the genome with ID "grch38_hs38d1_noalt" available from the Genome pulldown menu?

On Thu, Jan 11, 2018 at 5:27 PM, Brad Langhorst notifications@github.com wrote:

I've just captured fresh logs to eliminate the genome as a factor...

http://galaxy.neb.com/display_application/c1ce8522a94cd69a/ igv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151] Startup IGV Version 2.3.97 (157)07/10/2017 10:52 PM INFO [2018-01-11 20:14:41,120] [Main.java:152] Java 1.8.0_151 INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72] Fetching user directory... INFO [2018-01-11 20:14:41,274] [Main.java:153] Default User Directory: /Users/langhorst INFO [2018-01-11 20:14:41,274] [Main.java:154] OS: Mac OS X INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613] Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89] Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134] Download complete. Total bytes downloaded = 6418326 INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210] Genome loaded. id= hg19 INFO [2018-01-11 20:14:54,212] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 20:16:43,060] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 INFO [2018-01-11 20:16:43,070] [IGV.java:1684] Loading 1 resources. INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down INFO [2018-01-11 20:25:36,944] [Main.java:154] Startup IGV Version snapshot 01/09/2018 06:52 PM INFO [2018-01-11 20:25:36,944] [Main.java:155] Java 1.8.0_151 INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76] Fetching user directory... INFO [2018-01-11 20:25:37,019] [Main.java:156] Default User Directory: /Users/langhorst INFO [2018-01-11 20:25:37,019] [Main.java:157] OS: Mac OS X INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79] Enter genome combo box INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271] Genome loaded. id= hg19 INFO [2018-01-11 20:25:50,373] [CommandListener.java:120] Listening on port 60151 INFO [2018-01-11 20:26:02,501] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:748)

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[jrobinso]

The problem is the genome, not the lack of login dialog, that's a side-effect.

On Thu, Jan 11, 2018 at 5:43 PM, James Robinson <jrobinso@broadinstitute.org

wrote:

Hmm, somehow we're not communicating. If you start IGV stand-alone, no Galaxy, is the genome with ID "grch38_hs38d1_noalt" available from the Genome pulldown menu?

On Thu, Jan 11, 2018 at 5:27 PM, Brad Langhorst notifications@github.com wrote:

I've just captured fresh logs to eliminate the genome as a factor...

http://galaxy.neb.com/display_application/c1ce8522a94cd69a/i gv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151] Startup IGV Version 2.3.97 (157)07/10/2017 10:52 PM INFO [2018-01-11 20:14:41,120] [Main.java:152] Java 1.8.0_151 INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72] Fetching user directory... INFO [2018-01-11 20:14:41,274] [Main.java:153] Default User Directory: /Users/langhorst INFO [2018-01-11 20:14:41,274] [Main.java:154] OS: Mac OS X INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613] Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89] Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134] Download complete. Total bytes downloaded = 6418326 INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210] Genome loaded. id= hg19 INFO [2018-01-11 20:14:54,212] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 20:16:43,060] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 INFO [2018-01-11 20:16:43,070] [IGV.java:1684] Loading 1 resources. INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down INFO [2018-01-11 20:25:36,944] [Main.java:154] Startup IGV Version snapshot 01/09/2018 06:52 PM INFO [2018-01-11 20:25:36,944] [Main.java:155] Java 1.8.0_151 INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76] Fetching user directory... INFO [2018-01-11 20:25:37,019] [Main.java:156] Default User Directory: /Users/langhorst INFO [2018-01-11 20:25:37,019] [Main.java:157] OS: Mac OS X INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79] Enter genome combo box INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271] Genome loaded. id= hg19 INFO [2018-01-11 20:25:50,373] [CommandListener.java:120] Listening on port 60151 INFO [2018-01-11 20:26:02,501] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:748)

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[bwlang]

No that genome is not listed in my dropdown… but I don’t think that’s the problem. I’m loading data from that genome in galaxy to 2.3.92 and it is ale to load data (probably would wig out if I tried to address some chromosome that’s not present in bam file and the coordinates are probably all screwball)

Maye you’re checking the genome more carefully now? I’ll try to find a bam aligned to the hg19 genome to test that hypothesis.

On Jan 11, 2018, at 8:44 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

Hmm, somehow we're not communicating. If you start IGV stand-alone, no Galaxy, is the genome with ID "grch38_hs38d1_noalt" available from the Genome pulldown menu?

On Thu, Jan 11, 2018 at 5:27 PM, Brad Langhorst notifications@github.com<mailto:notifications@github.com> wrote:

I've just captured fresh logs to eliminate the genome as a factor...

http://galaxy.neb.com/display_application/c1ce8522a94cd69a/ igv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151] Startup IGV Version 2.3.97 (157)07/10/2017 10:52 PM INFO [2018-01-11 20:14:41,120] [Main.java:152] Java 1.8.0_151 INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72] Fetching user directory... INFO [2018-01-11 20:14:41,274] [Main.java:153] Default User Directory: /Users/langhorst INFO [2018-01-11 20:14:41,274] [Main.java:154] OS: Mac OS X INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613] Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89] Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134] Download complete. Total bytes downloaded = 6418326 INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210] Genome loaded. id= hg19 INFO [2018-01-11 20:14:54,212] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 20:16:43,060] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 INFO [2018-01-11 20:16:43,070] [IGV.java:1684] Loading 1 resources. INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down INFO [2018-01-11 20:25:36,944] [Main.java:154] Startup IGV Version snapshot 01/09/2018 06:52 PM INFO [2018-01-11 20:25:36,944] [Main.java:155] Java 1.8.0_151 INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76] Fetching user directory... INFO [2018-01-11 20:25:37,019] [Main.java:156] Default User Directory: /Users/langhorst INFO [2018-01-11 20:25:37,019] [Main.java:157] OS: Mac OS X INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79] Enter genome combo box INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271] Genome loaded. id= hg19 INFO [2018-01-11 20:25:50,373] [CommandListener.java:120] Listening on port 60151 INFO [2018-01-11 20:26:02,501] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2Fgalaxy.neb.com%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:748)

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[jrobinso]

Apparently, some undocumented hack has been used in the Galaxy setup to make this work in IGV 2.3.x. If that genome's not in your pulldown it should not be loadable, but there are ways to hack it.

If you can obtain the .genome file, place it in the folder "<user home>/igv/genomes, then restart IGV. That should work.

On Thu, Jan 11, 2018 at 5:48 PM, Brad Langhorst notifications@github.com wrote:

No that genome is not listed in my dropdown… but I don’t think that’s the problem. I’m loading data from that genome in galaxy to 2.3.92 and it is ale to load data (probably would wig out if I tried to address some chromosome that’s not present in bam file and the coordinates are probably all screwball)

Maye you’re checking the genome more carefully now? I’ll try to find a bam aligned to the hg19 genome to test that hypothesis.

On Jan 11, 2018, at 8:44 PM, Jim Robinson <notifications@github.com< mailto:notifications@github.com>> wrote:

Hmm, somehow we're not communicating. If you start IGV stand-alone, no Galaxy, is the genome with ID "grch38_hs38d1_noalt" available from the Genome pulldown menu?

On Thu, Jan 11, 2018 at 5:27 PM, Brad Langhorst <notifications@github.com< mailto:notifications@github.com>> wrote:

I've just captured fresh logs to eliminate the genome as a factor...

http://galaxy.neb.com/display_application/c1ce8522a94cd69a/ igv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151] Startup IGV Version 2.3.97 (157)07/10/2017 10:52 PM INFO [2018-01-11 20:14:41,120] [Main.java:152] Java 1.8.0_151 INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72] Fetching user directory... INFO [2018-01-11 20:14:41,274] [Main.java:153] Default User Directory: /Users/langhorst INFO [2018-01-11 20:14:41,274] [Main.java:154] OS: Mac OS X INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613] Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89] Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134] Download complete. Total bytes downloaded = 6418326 INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210] Genome loaded. id= hg19 INFO [2018-01-11 20:14:54,212] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 20:16:43,060] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default% 2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam& genome=grch38_hs38d1_noalt&merge=true&name=ControlLiver FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 INFO [2018-01-11 20:16:43,070] [IGV.java:1684] Loading 1 resources. INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/ igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down INFO [2018-01-11 20:25:36,944] [Main.java:154] Startup IGV Version snapshot 01/09/2018 06:52 PM INFO [2018-01-11 20:25:36,944] [Main.java:155] Java 1.8.0_151 INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76] Fetching user directory... INFO [2018-01-11 20:25:37,019] [Main.java:156] Default User Directory: /Users/langhorst INFO [2018-01-11 20:25:37,019] [Main.java:157] OS: Mac OS X INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79] Enter genome combo box INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271] Genome loaded. id= hg19 INFO [2018-01-11 20:25:50,373] [CommandListener.java:120] Listening on port 60151 INFO [2018-01-11 20:26:02,501] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com %2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default% 2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam& genome=grch38_hs38d1_noalt&merge=true&name=ControlLiver FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168)

at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341)

at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221)

at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:748)

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[bwlang]

Yep - seems to be that loading an hg19 bam to snapshot works fine

INFO [2018-01-11 20:47:54,096] [Main.java:154]  Startup  IGV Version snapshot 01/09/2018 06:52 PM
INFO [2018-01-11 20:47:54,097] [Main.java:155]  Java 1.8.0_151
INFO [2018-01-11 20:47:54,097] [DirectoryManager.java:76]  Fetching user directory...
INFO [2018-01-11 20:47:54,235] [Main.java:156]  Default User Directory: /Users/langhorst
INFO [2018-01-11 20:47:54,235] [Main.java:157]  OS: Mac OS X
INFO [2018-01-11 20:48:04,171] [GenomeManager.java:182]  Loading genome: /Users/langhorst/igv/genomes/hg19.genome
INFO [2018-01-11 20:48:08,395] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2018-01-11 20:48:08,405] [GenomeManager.java:271]  Genome loaded.  id= hg19
INFO [2018-01-11 20:48:08,585] [CommandListener.java:120]  Listening on port 60151
INFO [2018-01-11 20:49:07,775] [CommandListener.java:187]  GET /load?file=http%3A%2F%2Fgalaxy.neb.com<http://2Fgalaxy.neb.com>%2Fdisplay_application%2F8053ea43304606fd%2Figv_bam%2Flocal_default%2Fda9389bbcdaadbaa%2Fdata%2Fgalaxy_8053ea43304606fd.bam&genome=hg19&merge=true&name=Control_Lung_FS_Q5_A1.1.fastq.bam HTTP/1.1
INFO [2018-01-11 20:49:07,793] [IGV.java:1383]  Loading 1 resources.
INFO [2018-01-11 20:49:07,794] [TrackLoader.java:126]  Loading resource, path http://galaxy.neb.com/display_application/8053ea43304606fd/igv_bam/local_default/da9389bbcdaadbaa/data/galaxy_8053ea43304606fd.bam
INFO [2018-01-11 20:49:16,727] [HttpUtils.java:873]  Range-byte request succeeded
INFO [2018-01-11 20:49:29,587] [HttpUtils.java:873]  Range-byte request succeeded
INFO [2018-01-11 20:49:30,998] [AlignmentTrack.java:270]  Experiment type = OTHER

Maybe the fix here is just to complain that the proper genome could not be loaded… Sure would be nice if IGV could fetch the genome from galaxy - but I don’t think that’s a feature yet. Might be fun to grab bam headers and confirm that all the bam headers are present in the loaded genome’s headers with correct sizes.

Thanks!

Brad

On Jan 11, 2018, at 8:48 PM, Langhorst, Brad Langhorst@neb.com<mailto:Langhorst@neb.com> wrote:

No that genome is not listed in my dropdown… but I don’t think that’s the problem. I’m loading data from that genome in galaxy to 2.3.92 and it is ale to load data (probably would wig out if I tried to address some chromosome that’s not present in bam file and the coordinates are probably all screwball)

Maye you’re checking the genome more carefully now? I’ll try to find a bam aligned to the hg19 genome to test that hypothesis.

On Jan 11, 2018, at 8:44 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

Hmm, somehow we're not communicating. If you start IGV stand-alone, no Galaxy, is the genome with ID "grch38_hs38d1_noalt" available from the Genome pulldown menu?

On Thu, Jan 11, 2018 at 5:27 PM, Brad Langhorst notifications@github.com<mailto:notifications@github.com> wrote:

I've just captured fresh logs to eliminate the genome as a factor...

http://galaxy.neb.com/display_application/c1ce8522a94cd69a/ igv_bam/local_default log from 2.3.97, works fine, provides me a login prompt and loads the reads.

INFO [2018-01-11 20:14:41,120] [Main.java:151] Startup IGV Version 2.3.97 (157)07/10/2017 10:52 PM INFO [2018-01-11 20:14:41,120] [Main.java:152] Java 1.8.0_151 INFO [2018-01-11 20:14:41,121] [DirectoryManager.java:72] Fetching user directory... INFO [2018-01-11 20:14:41,274] [Main.java:153] Default User Directory: /Users/langhorst INFO [2018-01-11 20:14:41,274] [Main.java:154] OS: Mac OS X INFO [2018-01-11 20:14:44,425] [GenomeManager.java:613] Refreshing genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2018-01-11 20:14:44,426] [URLDownloader.java:89] Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome to /Users/langhorst/igv/genomes/hg19.genome.tmp INFO [2018-01-11 20:14:52,318] [URLDownloader.java:134] Download complete. Total bytes downloaded = 6418326 INFO [2018-01-11 20:14:52,335] [GenomeManager.java:163] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:14:54,155] [GenomeManager.java:210] Genome loaded. id= hg19 INFO [2018-01-11 20:14:54,212] [CommandListener.java:106] Listening on port 60151 INFO [2018-01-11 20:16:43,060] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2fgalaxy.neb.com/%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 INFO [2018-01-11 20:16:43,070] [IGV.java:1684] Loading 1 resources. INFO [2018-01-11 20:16:43,071] [TrackLoader.java:126] Loading resource, path http://galaxy.neb.com/display_application/c1ce8522a94cd69a/igv_bam/local_default/ee3dd54b74deb11b/data/galaxy_c1ce8522a94cd69a.bam INFO [2018-01-11 20:16:53,498] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:17:12,451] [HttpUtils.java:838] Range-byte request succeeded INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down

log from snapshot build, no login prompt,

INFO [2018-01-11 20:25:26,907] [ShutdownThread.java:51] Shutting down INFO [2018-01-11 20:25:36,944] [Main.java:154] Startup IGV Version snapshot 01/09/2018 06:52 PM INFO [2018-01-11 20:25:36,944] [Main.java:155] Java 1.8.0_151 INFO [2018-01-11 20:25:36,945] [DirectoryManager.java:76] Fetching user directory... INFO [2018-01-11 20:25:37,019] [Main.java:156] Default User Directory: /Users/langhorst INFO [2018-01-11 20:25:37,019] [Main.java:157] OS: Mac OS X INFO [2018-01-11 20:25:46,046] [GenomeManager.java:182] Loading genome: /Users/langhorst/igv/genomes/hg19.genome INFO [2018-01-11 20:25:50,250] [GenomeComboBox.java:79] Enter genome combo box INFO [2018-01-11 20:25:50,257] [GenomeManager.java:271] Genome loaded. id= hg19 INFO [2018-01-11 20:25:50,373] [CommandListener.java:120] Listening on port 60151 INFO [2018-01-11 20:26:02,501] [CommandListener.java:187] GET /load?file=http%3A%2F%2Fgalaxy.neb.comhttp://2fgalaxy.neb.com/%2Fdisplay_application%2Fc1ce8522a94cd69a%2Figv_bam%2Flocal_default%2Fee3dd54b74deb11b%2Fdata%2Fgalaxy_c1ce8522a94cd69a.bam&genome=grch38_hs38d1_noalt&merge=true&name=Control_Liver_FS_KapaPCR_C4.1.fastq_trim.nodupes_bam HTTP/1.1 ERROR [2018-01-11 20:26:02,570] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:168) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:341) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:221) at org.broad.igv.batch.CommandListener.run(CommandListener.java:126) at java.lang.Thread.run(Thread.java:748)

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[jrobinso]

Yes, I agree an error message should be presented here. Will add that.

Did you try downloading the genome file manually and placing it in the igv/genomes folder?

The correct way to do this from IGV's point of view is to send the full path (url) to the .genome file in the "genome" parameter of the URL, not a shorthand ID. However, that requires changes to Galaxy.

[bwlang]

OK.. I’ll look into a galaxy update to do this “properly”. We have all the information in galaxy so may not be a big deal to get this working.

Thanks again!

brad

On Jan 11, 2018, at 9:23 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

Yes, I agree an error message should be presented here. Will add that.

Did you try downloading the genome file manually and placing it in the igv/genomes folder?

The correct way to do this from IGV's point of view is to send the full path (url) to the .genome file in the "genome" parameter of the URL, not a shorthand ID. However, that requires changes to Galaxy.

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[jrobinso]

WRT verifying BAM headers, often people load bam files against other references on purpose, e.g. a GrCH38 fasta vs hg38, or a fasta with all the minor contigs vs one without them, or a fasta with different mitochondria or some additional viral genomes. A check is made and if nothing matches an error is presented.

[jrobinso]

So there are 2 supported options, (1) send the full URL to the .genome file, percent-encoded, rather than the I.D. (2) maintain your own "genome" server and change the URL to the server file in the advanced preferences. This replaces our server with yours, and you can use your own I.D.s. The disadvantage to this approach is you have to make the change for every IGV client, and you have to host all genomes not just your custom ones.

If you have further problems let me know.

On Thu, Jan 11, 2018 at 6:25 PM, Brad Langhorst notifications@github.com wrote:

OK.. I’ll look into a galaxy update to do this “properly”. We have all the information in galaxy so may not be a big deal to get this working.

Thanks again!

brad

On Jan 11, 2018, at 9:23 PM, Jim Robinson <notifications@github.com< mailto:notifications@github.com>> wrote:

Yes, I agree an error message should be presented here. Will add that.

Did you try downloading the genome file manually and placing it in the igv/genomes folder?

The correct way to do this from IGV's point of view is to send the full path (url) to the .genome file in the "genome" parameter of the URL, not a shorthand ID. However, that requires changes to Galaxy.

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[jrobinso]

BTW, it would be helpful to others if I knew how they were making this work with 2.3.x. One possibility is using the user-defined-genomes.txt list (or something to that effect). Could you look in your igv/genomes folder and see if that file exists, and if it does see if it has the problematic genome entry?

[bwlang]

Yep it exists…but not containing the grch38… genome. It only has genomes that I manually created.

brad

On Jan 11, 2018, at 9:49 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

BTW, it would be helpful to others if I knew how they were making this work with 2.3.x. One possibility is using the user-defined-genomes.txt list (or something to that effect). Could you look in your igv/genomes folder and see if that file exists, and if it does see if it has the problematic genome entry?

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[jrobinso]

Any other file in that folder with a pointer to that genome? I'm at a loss to know how 2.3.x gets the URL to the .genome file.

[bwlang]

cd ~/igv/genomes find . ./hg18.genome ./hg19.genome ./hg38.genome ./nc10.genome ./NC_000913.3.gbk ./seq ./user-defined-genomes.txt

Brad

On Jan 11, 2018, at 10:00 PM, Jim Robinson notifications@github.com<mailto:notifications@github.com> wrote:

Any other file in that folder with a pointer to that genome? I'm at a loss to know how 2.3.x gets the URL to the .genome file.

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[jrobinso]

OK, another place to search is the prefs.properties file in the igv folder. Any reference to the problematic genome there?

[bwlang]

I don't see anything... prefs.properties:

LAST_GENOME_IMPORT_DIRECTORY=/Users/langhorst/Documents/NEB/NGS/IGV Genome Files
SAM.SORT_OPTION=NUCLEOTIDE
SAM.HIDE_SMALL_INDEL=true
PORT_ENABLED=true
DEFAULT_GENOME_KEY=hg38
DEFAULT_FONT_FAMILY=Arial
GENOME_LIST=hg19;hg18;hg38;NC12;mc_controls
SAM.GROUP_OPTION=BASE_AT_POS
SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS=true
SAM.MAX_VISIBLE_RANGE=30000
SAM.DOWNSAMPLE_READS=false
SAM.BISULFITE_CONTEXT=NONE
SAM.QUICK_CONSENSUS_MODE=true
LAST_TRACK_DIRECTORY=/Users/langhorst/Documents/grch38_rrna
SAM.HIDDEN_TAGS=MD,SA,
org.broad.igv.plugin.bedtools:BEDTools:path=/usr/local/bin/bedtools
IGV.track.show.attribute.views=true
SAM.COLOR_BY=PAIR_ORIENTATION
DEFAULT_FONT_SIZE=12
SAM.LARGE_INSERTIONS_THRESOLD=5
SAM.SHOW_SOFT_CLIPPED=false
SAM.GROUP_BY_POS=ref0000773 9662293
SAM.SHOW_DUPLICATES=false
DEFINE_GENOME_INPUT_DIRECTORY_KEY=/Volumes/langhorst/genomes/eschColi_K12/seq
SAM.SMALL_INDEL_BP_THRESHOLD=10
SAM.FILTER_SECONDARY_ALIGNMENTS=true
SHOW_SEQUENCE_TRANSLATION=false
SAM.QUALITY_THRESHOLD=1
IGV.Bounds=42,34,1878,930
SAM.FLAG_UNMAPPED_PAIR=false
SAM.FLAG_LARGE_INDELS=false
DEFAULT_FONT_ATTRIBUTE=0
IGV.Frame.ExtendedState=0
IONTORRENT.RESULTS=http%3A%2F%2Fgalaxy.neb.com%2Fdisplay_application%2Ff31ed9fbd847ed18%2Figv_bam%2Flocal_default%2F9879886ce52a8675%2Fdata%2Fgalaxy_f31ed9fbd847ed18.bam

[jrobinso]

OK, I'm stumped. I might have to install Galaxy.

Did you try downloading the .genome file manually and placing it in igv/genomes? That should work.

Again, the most robust solution is to explicitly pass the url to the genome in the genome parameter, but it would be nice to understand how it was working before. Thanks for your help.

[jrobinso]

OK, I think I figured this out. I created a link to use with 2.3.92 that had a non-existent genome ID ("zzz"). Everything loaded, no errors, the bogus genome ID was just ignored. I suspect that's whats happening with you as well. You can test this by starting IGV and loading some other genome, mm10 or something, then loading your dataset with the problematic ID. My guess is the data is going to load, and the genome will remain mm10.