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jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
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no output file #14

Open Puputnik opened 6 years ago

Puputnik commented 6 years ago

Hello, my mobster run seems to be finished correctly, however i'm not getting any *_prediction.txt file

INFO 2018-06-19 11:26:34 SinglePassSamProgram Processed 47.000.000 records. INFO 2018-06-19 11:26:50 SinglePassSamProgram Processed 48.000.000 records. INFO 2018-06-19 11:27:07 SinglePassSamProgram Processed 49.000.000 records. INFO 2018-06-19 11:27:25 SinglePassSamProgram Processed 50.000.000 records. INFO 2018-06-19 11:27:41 ProcessExecutor null device INFO 2018-06-19 11:27:41 ProcessExecutor 1 [Tue Jun 19 11:27:41 CEST 2018] net.sf.picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 14,25 minutes. Runtime.totalMemory()=207618048 Exit value: 0 Exception in thread "main" java.lang.NumberFormatException: For input string: "378,964003" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at org.umcn.me.pairedend.Mobster.main(Mobster.java:96)

any clue?

Thanks a lot!

Puputnik commented 6 years ago

P.S. I forgot to say that the _hist.pdf and _insertstats files have been generated

jyhehir commented 6 years ago

Yes, I have seen this before. Probably your JVM is not installed with local english as default. Does this make sense?This can be overridden at the command lineeg -Duser.country=US -Duser.language=en Regards,Jayne On Tuesday, 19 June 2018, 11:43:39 am GMT+2, Puputnik notifications@github.com wrote:

Hello, my mobster run seems to be finished correctly, however i'm not getting any *_prediction.txt file

INFO 2018-06-19 11:26:34 SinglePassSamProgram Processed 47.000.000 records. INFO 2018-06-19 11:26:50 SinglePassSamProgram Processed 48.000.000 records. INFO 2018-06-19 11:27:07 SinglePassSamProgram Processed 49.000.000 records. INFO 2018-06-19 11:27:25 SinglePassSamProgram Processed 50.000.000 records. INFO 2018-06-19 11:27:41 ProcessExecutor null device INFO 2018-06-19 11:27:41 ProcessExecutor 1 [Tue Jun 19 11:27:41 CEST 2018] net.sf.picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 14,25 minutes. Runtime.totalMemory()=207618048 Exit value: 0 Exception in thread "main" java.lang.NumberFormatException: For input string: "378,964003" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at org.umcn.me.pairedend.Mobster.main(Mobster.java:96)

any clue?

Thanks a lot!

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Puputnik commented 6 years ago

tried with the -Duser.country=US -Duser.language=en options, still getting the same error unfortunately.

jyhehir commented 5 years ago

just to double check, which version of Mobster are you using. It really looks like the jvm is getting confused with the locales

jyhehir commented 5 years ago

Hello, Thanks for trying to suggested fix, I will look further into why the setting is not passed onto picard, internally.But in the mean time as a work around you could try to run pcard, for the insert size metrics, and then set this in mobster.properties. Regards,Jayne On Tuesday, 28 May 2019, 12:14:13 pm GMT+2, josesovaz notifications@github.com wrote:

Hello jyhehir,

I have exactly the same output error using the example provided:

WARNING 2019-05-28 12:07:30 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway. INFO 2019-05-28 12:07:33 SinglePassSamProgram Processed 1.000.000 records. INFO 2019-05-28 12:07:35 SinglePassSamProgram Processed 2.000.000 records. INFO 2019-05-28 12:07:36 SinglePassSamProgram Processed 3.000.000 records. INFO 2019-05-28 12:07:38 SinglePassSamProgram Processed 4.000.000 records. INFO 2019-05-28 12:07:39 SinglePassSamProgram Processed 5.000.000 records. INFO 2019-05-28 12:07:41 SinglePassSamProgram Processed 6.000.000 records. INFO 2019-05-28 12:07:42 SinglePassSamProgram Processed 7.000.000 records. INFO 2019-05-28 12:07:43 SinglePassSamProgram Processed 8.000.000 records. INFO 2019-05-28 12:07:45 SinglePassSamProgram Processed 9.000.000 records. INFO 2019-05-28 12:07:46 SinglePassSamProgram Processed 10.000.000 records. INFO 2019-05-28 12:07:48 SinglePassSamProgram Processed 11.000.000 records. INFO 2019-05-28 12:07:49 SinglePassSamProgram Processed 12.000.000 records. INFO 2019-05-28 12:07:50 SinglePassSamProgram Processed 13.000.000 records. INFO 2019-05-28 12:08:05 ProcessExecutor null device INFO 2019-05-28 12:08:05 ProcessExecutor 1 [Tue May 28 12:08:05 CEST 2019] net.sf.picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0,59 minutes. Runtime.totalMemory()=2039414784 Exit value: 0 Exception in thread "main" java.lang.NumberFormatException: For input string: "310,791697" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at org.umcn.me.pairedend.Mobster.configureAndRunPicard(Mobster.java:131) at org.umcn.me.pairedend.Mobster.main(Mobster.java:58)

I tried to solve this issue with the -Duser.country=US -Duser.language=en but it didn't work, it gives the same error again.

Regards,

Jose

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josesovaz commented 5 years ago

Finally, I could fix the issue. As you said, the problem was with the locale. I think If the locale is not in english as default, it gives the error because it can't recognize the "," instead of "." in the decimals.

I have set the locale in english using the following command in the terminal: export LANG=en_US.utf8

Then it works.

Thanks,

jose

jyhehir commented 5 years ago

Excellent, thanks for working it out. On Friday, 31 May 2019, 3:57:41 pm GMT+2, josesovaz notifications@github.com wrote:

Finally, I could fix the issue. As you said, the problem was with the locale. I think If the locale is not in english as default, it gives the error because it can't read the "," instead of "." in the decimal.

I have set the locale in english using the following command in the terminal: export LANG=en_US.utf8

Then it works.

Thanks,

jose

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