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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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PeptideProphet parsers not found #201

Closed aezimmerman closed 3 years ago

aezimmerman commented 3 years ago

I am new to Philosopher, and tried to run PeptideProphet on a linux cluster using a database generated with Philosopher and pepXML output from an MSFragger search, but got the following error that I'm uncertain how to address. I extracted the philosopher_v3.4.13_linux_amd64.zip release to use Philosopher on the server. Any recommendations would be appreciated.

Thanks very much, Amy

OS information: LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Description: Red Hat Enterprise Linux Workstation release 6.6 (Santiago)

(philos_env) [zimm824@constance01 ~]$ ./philosopher workspace --init INFO[19:55:22] Executing Workspace v3.4.13
INFO[19:55:23] Creating workspace
INFO[19:55:23] Done
(philos_env) [zimm824@constance01 ~]$ ./philosopher peptideprophet --database EndoPop/Data/ref/2021-04-07-decoys-contam-2615840639.genes.faa.fas --ppm --accmass --expectscore --decoyprobs --nonparam EndoPop/Data/N15_fragger_all_2021-04-14/Endopop_Proteomics_1_31Mar21_Merry_20-11-14/Endopop_Proteomics_1_31Mar21_Merry_20-11-14.pepXML INFO[20:06:10] Executing PeptideProphet v3.4.13
/tmp/da53fa22-ac3f-453b-9ded-c7dd497beb13/InteractParser: /lib64/libc.so.6: version GLIBC_2.17' not found (required by /tmp/da53fa22-ac3f-453b-9ded-c7dd497beb13/InteractParser) /tmp/da53fa22-ac3f-453b-9ded-c7dd497beb13/InteractParser: /lib64/libc.so.6: versionGLIBC_2.14' not found (required by /tmp/da53fa22-ac3f-453b-9ded-c7dd497beb13/InteractParser)

fabianegli commented 3 years ago

Hi Amy, you might want to check the documentation of the cluster you use to see if you need to load some module before you can run C code. The cluster I have access to sometimes provides multiple module versions and you might need to choose a newer one. If the file /lib64/libc.so.6 exists, you can check from which package it originates by rpm -qf /lib64/libc.so.6. It should give you a string with the version number of the installed glibc version.

aezimmerman commented 3 years ago

Thank you for your assistance. I'll work with the cluster administrator to get this sorted out.