alekseyzimin
commented
4 years ago It is likely that you have another version of samtools in your $PATH, please check your environment
Open fairquestion opened 4 years ago
alekseyzimin
commented
4 years ago It is likely that you have another version of samtools in your $PATH, please check your environment
JWDebler
commented
2 years ago I am also getting this error. I have the same version of samtools installed as the install script installs. I get the same error when I change my PATH to use masurca's install of samtools 1.13
alekseyzimin
commented
2 years ago Hi,
Polca uses samtools version 0.1.20. Can you check your LD_LIBRARY_PATH variable on your system? It may be looking for libraries in the wrong place. You can also check "ldd MaSuRCA-x.x.x/bin/samtools"
Best, Aleksey
On Thu, Dec 2, 2021 at 4:29 AM Johannes Debler @.***> wrote:
I am also getting this error. I have the same version of samtools installed as the install script installs. I get the same error when I change my PATH to use masurca's install of samtools 1.13
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JWDebler
commented
2 years ago Hi,
LD_LIBRARY_PATH doesn't seem to be set. What should it be pointing at?
alekseyzimin
commented
2 years ago Ok, this is good. Can you verify that samtools in masurca bin exists and working?
On Thu, Dec 2, 2021 at 8:39 AM Johannes Debler @.***> wrote:
Hi,
LD_LIBRARY_PATH doesn't seem to be set. What should it be pointing at?
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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com
JWDebler
commented
2 years ago It does exist, but when I try to run it I get the already mentioned error:
/opt/masurca/current/bin$ ./samtools ./samtools: error while loading shared libraries: libbam.so.0: cannot open shared object file: No such file or directory
alekseyzimin
commented
2 years ago OK, I think I see a problem here. MaSuRCA installs samtools in its own bin folder. The path cannot be /opt/masurca/current/bin, it has to be
JWDebler
commented
2 years ago it is in /opt/masurca/MaSuRCA-4.0.5/bin. I do have a symbolic link current in /opt/masurca/ pointing to MaSuRCA-4.0.5 currently. That way I can have several versions of tools installed, but current always points to the latest version.
I get the same error when I don't use the symbolic link though.
/opt/masurca/MaSuRCA-4.0.5/bin$ ./samtools ./samtools: error while loading shared libraries: libbam.so.0: cannot open shared object file: No such file or directory
JWDebler
commented
2 years ago OK, I fixed it. The first time I installed masurca it was somewhere else and I then moved the whole folder to its current location. That seems to have broken something. I just installed it again from scratch and now it works.
alekseyzimin
commented
2 years ago Great! The solution was to re-install MaSuRCA. MaSuRCA is portable, but the whole installation folder must remain intact.
On Thu, Dec 2, 2021 at 12:44 PM Johannes Debler @.***> wrote:
OK, I fixed it. The first time I installed masurca it was somewhere else and I then moved the whole folder to its current location. That seems to have broken something. I just installed it again from scratch and now it works.
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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com
Dear all,
When running Polca (but also when running the samtools file located in bin) I am getting this error:
samtools: error while loading shared libraries: libbam.so.0: cannot open shared object file: No such file or directory.
Actually there is no libbam.so.0 in the share folder, although the installation was completely ok without error. What is happening?