Open issues in InterProScan¶
This page documents the latest list of known issues, and we are working to fix them as soon as possible. For assistance with other InterProScan problems, please contact us using EMBL EBI’s support form.
1. CDD/RPSBlast errors¶
On some linux systems, you may get rpsblast errors like
bin/blast/ncbi-blast-2.10.1+/rpsbproc: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory
The missing library is libgomp1. On Ubuntu you might install it as follows:
sudo apt-get install -y libgomp1
On other systems, you have similar installation commands
2. Coils errors¶
If you see an error concerning Coils, for example the error below, it means the binary we provide is not compatible with your system.
Cannot run program ".../bin/ncoils/2.2.1/ncoils": error=2, No such file or directory
In this case, you may need to compile the Coils binary and it is straight forward as follows.
cp src/coils/ncoils/2.2.1/ncoils bin/ncoils/2.2.1/ncoils
These steps should update the Coils binary.
3. Prosite/pfsearchV3 errors¶
On some linux systems, you may get pfsearchV3 errors like
Error output from binary: bin/prosite/pfsearchV3: error while loading shared libraries: libpcre2.so: cannot open shared object file: No such file or directory
The missing library is pcre2. On Ubuntu you might install it as follows:
sudo apt-get install -y libpcre2-dev
On other systems, you have similar installation commands.
Additionally on some systems, specially on cluster environments, the following error has been reported
Error setting affinity!
Error running prosite binary bin/prosite/pfsearchV3
This means the provided binary is not compatible with your system. We have included alternative binaries that you can try, by updating you interproscan.properties file to point to the alternative binaries:
If the problem persist, you may need to compile those binaries from source, making sure to build without affinity by compiling with the flag
cmake -DUSE_AFFINITY=OFF ..
4. HMMER errors¶
The HMM libraries provided by some member databases (SUPERFAMILY and SFLD) are not compatible with newer HMMER versions and an error will occur when those libraries are being indexed by hmmpress version greater than ‘3.1b1’. To avoid this issue we recommend using the HMMER binaries bundled with interproscan.
If you encounter errors not listed above, please contact us using EMBL EBI’s support form.
please give us enough background information when you contact us, such as:
the linux distribution and version
the InterProScan version
the java version
command line used
the complete error log if possible