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schatzlab / crossstitch

Code for phasing SVs with SNPs
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Installation problem #6

Open CWYuan08 opened 5 years ago

CWYuan08 commented 5 years ago

Dear schatzlab, I want to run 'refineinsertions' of crossstitch on our cluster, I have installation problem as follows: when I installed the package, after typing last 'make' I got "Compiling vcf2diploid javac -d classes VCF2diploid.java Error occurred during initialization of VM Could not reserve enough space for object heap Could not create the Java virtual machine. make: *** [compile] Error 1"

When I tried ' ./refineinsertion.sh' I got: "rm: cannot remove `crossstitch/src/csout_19410/*': No such file or directory Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=8 Error occurred during initialization of VM Could not reserve enough space for object heap Could not create the Java virtual machine."

Could you please help me on using crossstitch?

Thank you very much Best, Ulrika

mschatz commented 5 years ago

Hi Ulrika,

Looks like you have a problem with your java compiler - unfortunately this is very system specific so you will have to work with your local IT to get it resolved

Good luck

Mike

On Fri, Dec 28, 2018 at 6:49 PM ChengweiUlrikaYuan notifications@github.com wrote:

Dear schatzlab, I want to run 'refineinsertions' of crossstitch on our cluster, I have installation problem as follows: when I installed the package, after typing last 'make' I got "Compiling vcf2diploid javac -d classes VCF2diploid.java Error occurred during initialization of VM Could not reserve enough space for object heap Could not create the Java virtual machine. make: *** [compile] Error 1"

When I tried ' ./refineinsertion.sh' I got: "rm: cannot remove `crossstitch/src/csout_19410/*': No such file or directory Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=8 Error occurred during initialization of VM Could not reserve enough space for object heap Could not create the Java virtual machine."

Could you please help me on using crossstich?

Thank you very much Best, Ulrika

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CWYuan08 commented 5 years ago

Dear Mike, thank you very much

CWYuan08 commented 5 years ago

Dear Mike, I have managed to install it on our LSF system; I have encountered new problems when running refine insertion.sh: it kept reporting files in the csout folder": No such file or directory" and "Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=8 cannot allocate memory for thread-local data: ABORT"

Why this is? Thank you again Ulrika

mschatz commented 5 years ago

It still sounds like a java issue which are very system specific. refine_insertions.sh is just a simple shell script, so you may need to adjust the settings for RAM and/or cores to match your local infrastructure

Good luck

Mike

On Tue, Mar 5, 2019 at 6:42 AM CWYuan08 notifications@github.com wrote:

Dear Mike, I have managed to install it on our LSF system; I have encountered new problems when running refine insertion.sh: it kept reporting files in the csout folder": No such file or directory" and "Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=8 cannot allocate memory for thread-local data: ABORT"

Why this is? Thank you again Ulrika

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/schatzlab/crossstitch/issues/6#issuecomment-469649799, or mute the thread https://github.com/notifications/unsubscribe-auth/AAL98w9Q8AJ_QKglUfebsJ_M_MCgkdCqks5vTlg_gaJpZM4ZkT8J .