errors running sortsamerefname, biostar154220

[PAMorin]

Verify

• if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
• the version of java 1.8

Subject of the issue

Following format from http://lindenb.github.io/jvarkit/Biostar154220.html. If I run with "-T bam" in the command line as given: java -jar ~/jvarkit/dist/sortsamrefname.jar -T bam z0186934_Psin_unique_w_header.bam | java -jar ~/jvarkit/dist/biostar154220.jar -n 400 -T bam | /usr/local/samtools-1.2/bin/samtools sort z0186934_Psin_maxDP400

I get errors about too many parameters: [SEVERE][Launcher]There was an error in the command line arguments. Please check your parameters : Expected one or zero argument but got 3 : [-T, bam, z0186934_Psin_unique_w_header.bam] [INFO][Launcher]sortsamrefname Exited with failure (-1) [SEVERE][Launcher]There was an error in the command line arguments. Please check your parameters : Expected one or zero argument but got 2 : [-T, bam] [INFO][Launcher]biostar154220 Exited with failure (-1)

If I run without "-T bam" (since this is not a listed option, but is in the example) java -jar ~/jvarkit/dist/sortsamrefname.jar z0186934_Psin_unique_w_header.bam | java -jar ~/jvarkit/dist/biostar154220.jar -n 400 | /usr/local/samtools-1.2/bin/samtools sort z0186934_Psin_maxDP400

I get a different error: [SEVERE][Launcher]/tmp/snappy-1.1.4-f9062b84-b01a-4186-9495-556df5f44618-libsnappyjava.so: /tmp/snappy-1.1.4-f9062b84-b01a-4186-9495-556df5f44618-libsnappyjava.so: failed to map segment from shared object: Operation not permitted [INFO][Launcher]sortsamrefname Exited with failure (-1)

Your environment

• version of jvarkit
• version of java
• the value of ${JAVA_HOME}
• which OS; Red Hat Enterprise Linux 6 (64 bit)

Steps to reproduce

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Expected behaviour

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Actual behaviour

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[lindenb]

my bad : the example for biostar154220 was outdated. Please check the updated manuals for sortsamrefname and biostar154220 . in you case the option -T was replaced with --samoutputformat BAM

[lindenb]

for the other error:

failed to map segment from shared object: Operation not permitted`

this is not dependent of jvarkit. e.g; (googled the error message) : Check you have the rights to write in tmp, the partitions, etc...