ngchm object can't be generated

[Sa753]

Dear team,

Thank you for the useful tool. I managed to generate the infercnv_object guided by the 2steps approach as in the tutorial. when I tried to use the resulting object as input to ngchm function, it generates one of the following 2 errors:

1- if I set the out_dir to a new folder, I get the following error: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './infercnv.observation_groupings.txt': No such file or directory

I definitely have the infercnv.observation_groupings.txt file in the output of infercnv

2- if I set the out_dir to the same output_dir of the infercnv function, I get the following error

Sun Sep 05 22:06:25 2021 PROGRESS :Writing specification: 50 creating specification directory Sun Sep 05 22:06:25 2021 PROGRESS :Writing specification: 80 writing extra support files Exception in thread "main" java.lang.UnsupportedClassVersionError: mda/ngchm/datagenerator/ShaidyRMapGen : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637) at java.lang.ClassLoader.defineClass(ClassLoader.java:621) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141) at java.net.URLClassLoader.defineClass(URLClassLoader.java:283) at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) Error in NGCHM::chmExportToFile(hm, file_path, overwrite = TRUE, shaidyMapGen = path_to_shaidyMapGen) : export to ngchm failed

I have the following versions

NGCHM version 0.12.6 infercnv version 1.9.1 infercnvNGCHM version 0.1.1

Could you please help?

Thanks

[brianjohnhaas]

@Maxwell Brown @.***> - any ideas?

On Sun, Sep 5, 2021 at 5:17 PM Sa753 @.***> wrote:

Dear team,

Thank you for the useful tool. I managed to generate the infercnv_object guided by the 2steps approach as in the tutorial. when I tried to use the resulting object as input to ngchm function, it generates one of the following 2 errors:

1- if I set the out_dir to a new folder, I get the following error: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './infercnv.observation_groupings.txt': No such file or directory

I definitely have the infercnv.observation_groupings.txt file in the output of infercnv

2- if I set the out_dir to the same output_dir of the infercnv function, I get the following error

Sun Sep 05 22:06:25 2021 PROGRESS :Writing specification: 50 creating specification directory Sun Sep 05 22:06:25 2021 PROGRESS :Writing specification: 80 writing extra support files Exception in thread "main" java.lang.UnsupportedClassVersionError: mda/ngchm/datagenerator/ShaidyRMapGen : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637) at java.lang.ClassLoader.defineClass(ClassLoader.java:621) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141) at java.net.URLClassLoader.defineClass(URLClassLoader.java:283) at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) Error in NGCHM::chmExportToFile(hm, file_path, overwrite = TRUE, shaidyMapGen = path_to_shaidyMapGen) : export to ngchm failed

I have the following versions

NGCHM version 0.12.6 infercnv version 1.9.1 infercnvNGCHM version 0.1.1

Could you please help?

Thanks

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

[Sa753]

Hi Team,

Any suggestions please?

[brownmp]

Hello @Sa753

The out_dir parameter for the ngchm() function should be set to the out directory used for your infercnv run. The file infercnv.observation_groupings.txt should be present in the out_dir. This is ambiguous in the documentation.

What commands are you using to create the infercnv NGCHM?

Best, M.Brown

[ChrisWakefield]

Hello @Sa753 Exception in thread "main" java.lang.UnsupportedClassVersionError: mda/ngchm/datagenerator/ShaidyRMapGen : Unsupported major.minor version 52.0

occurs when trying to run "ShaidyRMapGen" in an older version of java than what it was compiled for. Version 52 is JDK 1.8, which is far behind the latest. If you can upgrade to at least Java 1.8, you should not see that problem. Since there had been no further comments for ~6 months, I'd guess this was already figured out or abandoned, so I suggest closing this issue.