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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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Test run issues: Picard error and MobileInsertions-1.0-SNAPSHOT.jar does not exist #29

Closed npaulat closed 4 years ago

npaulat commented 4 years ago

Hello,

I have just installed Mobster, and did not notice any errors during installation. However, when trying to run Mobster with the sample bam command cd target java -Xmx8G -jar MobileInsertions-0.2.4.1.jar \ -properties Mobster.properties \ -out TestSample

I receive the following error:

java -Xmx8G -jar MobileInsertions-0.2.4.1.jar -properties Mobster.properties -out TestSample [Thu Aug 22 10:14:52 CDT 2019] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=TestSample_hist.pdf INPUT=../test_files/chr12_wgs_3000ins_100excl_10x_bwadef.bam OUTPUT=TestSample_insertstats STOP_AFTER=50000000 VALIDATION_STRINGENCY=LENIENT DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Aug 22 10:14:52 CDT 2019] Executing as npaulat@compute-7-16 on Linux 3.10.0-693.21.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Picard version: 1.73(1234) WARNING 2019-08-22 10:14:52 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway. INFO 2019-08-22 10:14:55 SinglePassSamProgram Processed 1,000,000 records. INFO 2019-08-22 10:14:57 SinglePassSamProgram Processed 2,000,000 records. INFO 2019-08-22 10:14:59 SinglePassSamProgram Processed 3,000,000 records. INFO 2019-08-22 10:15:02 SinglePassSamProgram Processed 4,000,000 records. INFO 2019-08-22 10:15:04 SinglePassSamProgram Processed 5,000,000 records. INFO 2019-08-22 10:15:06 SinglePassSamProgram Processed 6,000,000 records. INFO 2019-08-22 10:15:08 SinglePassSamProgram Processed 7,000,000 records. INFO 2019-08-22 10:15:10 SinglePassSamProgram Processed 8,000,000 records. INFO 2019-08-22 10:15:13 SinglePassSamProgram Processed 9,000,000 records. INFO 2019-08-22 10:15:15 SinglePassSamProgram Processed 10,000,000 records. INFO 2019-08-22 10:15:17 SinglePassSamProgram Processed 11,000,000 records. INFO 2019-08-22 10:15:19 SinglePassSamProgram Processed 12,000,000 records. INFO 2019-08-22 10:15:21 SinglePassSamProgram Processed 13,000,000 records. [Thu Aug 22 10:15:39 CDT 2019] net.sf.picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.78 minutes. Runtime.totalMemory()=1912602624 FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page Exception in thread "main" net.sf.picard.PicardException: Unexpected exception executing [Rscript /tmp/npaulat/script2642089209349607558.R /lustre/work/npaulat/mobster/target/TestSample_insertstats /lustre/work/npaulat/mobster/target/TestSample_hist.pdf chr12_wgs_3000ins_100excl_10x_bwadef.bam] at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:102) at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:78) at net.sf.picard.util.RExecutor.executeFromFile(RExecutor.java:73) at net.sf.picard.util.RExecutor.executeFromClasspath(RExecutor.java:55) at net.sf.picard.analysis.CollectInsertSizeMetrics.finish(CollectInsertSizeMetrics.java:133) at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:145) at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:82) Caused by: java.io.IOException: Cannot run program "Rscript": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:620) at java.lang.Runtime.exec(Runtime.java:485) at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:93) ... 9 more Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 12 more Exit value: 1

It then continues on with other steps, which appear to run without error.

In addition, when trying to run java -Xmx8G -jar MobileInsertions-1.0-SNAPSHOT.jar \ -properties Mobster_latest.properties \ -in input.bam \ -sn test_sample \ -out mobster_test

I get: "Error: Unable to access jarfile MobileInsertions-1.0-SNAPSHOT.jar" I can't figure out where the MobileInsertions-1.0-SNAPSHOT.jar or the Mobster_latest.properties file would exist either.

Any help would be greatly appreciated.

meboussaha commented 4 years ago

Dear npaulat, I was wondering whether you have solved your issue and where did you find MobileInsertions-1.0-SNAPSHOT.jar? Thank you for your response Mekki

npaulat commented 4 years ago

I solved the issue. The MobileInsertions-1.0-SNAPSHOT.jar is just the old name for the MobileInsertions-0.2.4.1.jar, and was not updated in the example commands in the README. As for the Picard errors, they are warnings from some sort of utility, but Mobster still runs to completion.

meboussaha commented 4 years ago

OK thanks a lot for the tip. I also figure dit out lately by testing the MobileInsertions-0.2.4.1.jar and option bwa-mem. Cheers

De : npaulat notifications@github.com Envoyé : mercredi 6 novembre 2019 00:07 À : jyhehir/mobster mobster@noreply.github.com Cc : Mekki Boussaha mekki.boussaha@inra.fr; Comment comment@noreply.github.com Objet : Re: [jyhehir/mobster] Test run issues: Picard error and MobileInsertions-1.0-SNAPSHOT.jar does not exist (#29)

I solved the issue. The MobileInsertions-1.0-SNAPSHOT.jar is just the old name for the MobileInsertions-0.2.4.1.jar, and was not updated in the example commands in the README. As for the Picard errors, they are warnings from some sort of utility, but Mobster still runs to completion.

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