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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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error while loading shared libraries: libhts.so.2 #101

Closed kpatankar closed 5 years ago

kpatankar commented 6 years ago

Hi,

I installed pindel. When I run the ./pindel command it gives me following error.

./pindel: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory

To resolve this I performed following steps: find ~ -name libhts.so.2

It gave me the following path /home/kalyani/bin/htslib-1.9/libhts.so.2

export LD_LIBRARY_PATH=/home/kalyani/htslib-1.6/libhts.so.2

It still gives me the error regarding the htslib.so.2 not found.

Are there some steps which I am missing? Appreciate your response.

Thanks!!!

kpatankar commented 6 years ago

Hi,

The issue was resolved by command:

export LD_LIBRARY_PATH=/home/kalyani/htslib-1.6/

./pindel running successfully.

luistatlav commented 5 years ago

I had a similar problem with the program gencore:

./gencore

./gencore: error while loading shared libraries: libhts.so.2to3part5: cannot open shared object file: No such file or directory

Thanks for you command. It resolved the problem.

Yuxinagli commented 5 years ago

hi, luistatlav. I have the same problem with yours. How did you solve it since it's libhts.so.2to3part5 missing not the libhts.so? Thanks!!

luistatlav commented 5 years ago

hi, luistatlav. I have the same problem with yours. How did you solve it since it's libhts.so.2to3part5 missing not the libhts.so? Thanks!!

Hi @Yuxinagli, I had the problem on subsystem of linux for Windows. I did the same that @kpatankar:

The issue was resolved by command: export LD_LIBRARY_PATH=/home/NameOfUser/htslib-1.6/

and ./gencore running successfully.

Yuxinagli commented 5 years ago

hi, luistatlav. I have the same problem with yours. How did you solve it since it's libhts.so.2to3part5 missing not the libhts.so? Thanks!!

Hi @Yuxinagli, I had the problem on subsystem of linux for Windows. I did the same that @kpatankar:

The issue was resolved by command: export LD_LIBRARY_PATH=/home/NameOfUser/htslib-1.6/

and ./gencore running successfully.

Thanks, @luistatlav ! It works with this modification in the ~/.bashrc .