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Trimmomatic and Salmon error

Hello I submitted my script in Slurm to process Salmon and Trimmomatic. I checked the Salmon and Trimmomatic version, the script should be all right, but I still ran into error messages when I checked the tail log. Are those addressed something wrong with the Salmon in slurm?

$ tail log

Unable to access jarfile trimmomatic
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by salmon)
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/applications/spack/applications/gcc-8.2.0/intel-tbb-2019-vfqbzt4vtydsvty66tg7azlsjtfaon6v/lib/libtbbmalloc_debug.so.2)
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/applications/spack/applications/gcc-8.2.0/intel-tbb-2019-vfqbzt4vtydsvty66tg7azlsjtfaon6v/lib/libtbb_debug.so.2)
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libgomp.so.1)
salmon: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libgomp.so.1)
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libstdc++.so.6)
salmon: /lib64/libc.so.6: version `GLIBC_2.16' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libstdc++.so.6)
salmon: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libstdc++.so.6)
salmon: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/applications/spack/applications/gcc-4.8.5/gcc-8.2.0-sxbf4jq6ghmoybsjlpqz2dm2qbbxzfyn/lib64/libgcc_s.so.1)`
rna-seq
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updated by h.mon h.mon • written by slin023 • slin023

1 answer

It looks like you have an inconsistent set of modules loaded on the nodes where younare running? Can you run the software successfully from the submit node? If so, then you need to replicate the loased modules and paths in your job script. It's usually a bit more pain to get thimgs working across cluster nodes, but this is why most clusters provide module aystems to ensure uniform environments for running software.

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written by Rob Rob

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