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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Segmentation fault (core dumped) #28

Closed iichelhadi closed 3 years ago

iichelhadi commented 3 years ago

Hi all, I am trying to run msisensor-pro scan to get a list of msi sites but keep getting "Segmentation fault (core dumped)" error. I running this on a HPC cluster with 40gb of RAM so I don't think it should be a memory issue. hope to get somehelp.

regards

PengJia6 commented 3 years ago

Hi,

@iichelhadi Which version of msisensor-pro did you use and how did you install msisensor-pro?

best, Peng

iichelhadi commented 3 years ago

Hi,

@iichelhadi Which version of msisensor-pro did you use and how did you install msisensor-pro?

best, Peng

thanks for the reply. I installed version 1.0.2 and I installed it using conda conda install msisensor-pro

PengJia6 commented 3 years ago

There were also similar error before version 1.2.0 (#16). Could you please try the lastet version(1.2.0).

PS: Maybe, you need to install the 1.2.0 by docker or build by yourself. And you can also try to run the binary file, if you use ubuntu system.

iichelhadi commented 3 years ago

There were also similar error before version 1.2.0 (#16). Could you please try the lastet version(1.2.0).

PS: Maybe, you need to install the 1.2.0 by docker or build by yourself. And you can also try to run the binary file, if you use ubuntu system.

I don't have admin privileges on the HPC so I can only install the version that is available in anaconda

PengJia6 commented 3 years ago

@iichelhadi Could you please use the binary version? You can download it directly from here.

iichelhadi commented 3 years ago

@iichelhadi Could you please use the binary version? You can download it directly from here.

thnk you. Not sure how to use it

PengJia6 commented 3 years ago

@iichelhadi

Please run the following commads! 

wget https://github.com/xjtu-omics/msisensor-pro/raw/master/binary/msisensor-pro    
chmod +x msisensor-pro     
./msisensor-pro
PengJia6 commented 3 years ago

@iichelhadi

Is that all right?

iichelhadi commented 3 years ago

@iichelhadi

Is that all right?

apologies. having an issue with a different library when I try to run it I get the following error: ./msisensor-pro: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

i have contacted our IT department to resolve this issue.

PengJia6 commented 3 years ago

@iichelhadi Sorry for the bad installation, I have pull a request in bioconda to support msisensor-pro:v1.2.0 installation with conda. Please install msisensor-pro with 

conda install msisensor-pro
iichelhadi commented 3 years ago

@iichelhadi Sorry for the bad installation, I have pull a request in bioconda to support msisensor-pro:v1.2.0 installation with conda. Please install msisensor-pro with

conda install msisensor-pro

I did as you mentioned. The version installed is v1.0.2 instead of v1.2.0

PengJia6 commented 3 years ago

@iichelhadi Thanks for your patient!