Missing libz so file

[bernt-matthias]

Describe the bug

I'm using philosopher from within the sipros pipeline. There I get the following error about a missing shared libraries: libz.so.1. The so file is available, i.e. find / -iname "libz.* gives me

/usr/local/lib/libz.so.1.3.1
/usr/local/lib/libz.so.1
/usr/local/lib/libz.a
/usr/local/lib/libz.so

2025-12-17 15:16:00,062 - sipros_workflow - INFO - Running command: /usr/local/bin/philosopher workspace --clean --nocheck && /usr/local/bin/philosopher workspace --init --nocheck --temp /tmp/tmpfwk0cw25/tmp/philosopher_tmp && /usr/local/bin/philosopher proteinprophet --maxppmdiff 2000000 --output combined test_sample_bacteria_2.raw_download_1/test_sample_bacteria_2.raw_download_1.pep.xml test_sample_bacteria_1.raw_download_1/test_sample_bacteria_1.raw_download_1.pep.xml test_sample_bacteria_3.raw_download_1/test_sample_bacteria_3.raw_download_1.pep.xml && /usr/local/bin/philosopher database --annotate targetDecoy.faa --prefix Decoy_ && /usr/local/bin/philosopher filter --sequential --prot 0.01 --picked --tag Decoy_ --pepxml pepxmls --protxml combined.prot.xml --razor && /usr/local/bin/philosopher report
2025-12-17 15:16:00,226 - sipros_workflow - ERROR - Command execution failed: time="15:16:00" level=info msg="Executing Workspace  v5.1.2"
time="15:16:00" level=info msg="Removing workspace"
time="15:16:00" level=info msg=Done
time="15:16:00" level=info msg="Executing Workspace  v5.1.2"
time="15:16:00" level=info msg="Creating workspace"
time="15:16:00" level=info msg=Done
time="15:16:00" level=info msg="Executing ProteinProphet  v5.1.2"
/tmp/tmpfwk0cw25/tmp/philosopher_tmp/ProteinProphet: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
time="15:16:00" level=error msg="Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files"

I was able to workarounbd with export LD_LIBRARY_PATH=/usr/local/lib:\$LD_LIBRARY_PATH but this seems to be not the proper fix.

To Reproduce

I'm running in this container: docker pull quay.io/biocontainers/sipros:5.0.1--hdfd78af_0

Should also be reproducible in docker pull quay.io/biocontainers/philosopher:5.1.2--he881be0_0

Please complete the following information:

• OS: Linux

[anesvi]

We are not familiar with the sipros pipeline, so there is very little we can help. Please use our FragPipe pipeline which is being continuously developed and well supported.

[bernt-matthias]

The error seems to be independent of sipros. The first line of the log contains the philosopher call.

Out of interest, does FragPipe support SIP analyses? I already advertised FragPipe in our institute .. maybe this is another opportunity.

[anesvi]

I am sorry I do not know what SIP is.

[bernt-matthias]

Proteomic stable isotope probing (SIP) is a technique used in microbial ecology to trace non-radioactive isotopes from labeled substrates into newly synthesized proteins of specific microorganisms. This method helps identify which microbes are actively metabolizing certain nutrients in complex communities.

[anesvi]

Thanks. At any rate, we cannot help with running philosopher pipeline outside of FragPipe at this time. Please try FragPipe m, perhaps you can what you need.