ProteinProphet: 'std::runtime_error' -what(): locale::facet::_S_create_c_locale name not valid time="15:20:59" level=fatal msg="Cannot execute program. There was an error with ProteinProphet, please check your parameters and input files"

[jjGG]

Dear Developers

Describe the bug
I reproducibly get an error with ProteinProphet using FragPipeGUI 14. I tried already different databases (human, mouse) (always with splittingDB option) before I would like to run my huge metaProteomics database.
Human and mouse were downloaded and annotated by philosopher as described in the tutorial. I am aware that using these DBs I will mostly identify contaminant proteins in these samples.. Nevertheless I should not run into an error.

ProteinProphet [Work dir: /scratch/j_p3635_wFragPipe/outputFresh]
/scratch/FragPipe14/philosopher proteinprophet --maxppmdiff 2000000 --output combined /scratch/j_p3635_wFragPipe/outputFresh/j_p3635_wFragPipe/interact.pep.xml
time="15:20:58" level=info msg="Executing ProteinProphet v3.3.11"
terminate called after throwing an instance of 'std::runtime_error'
what(): locale::facet::S_create_c_locale name not valid
time="15:20:59" level=fatal msg="Cannot execute program. There was an error with ProteinProphet, please check your parameters and input files"
Process 'ProteinProphet' finished, exit code: 1
Process returned non-zero exit code, stoppingProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906251008-exported (Linux-x86_64))
PhilosopherDbAnnotate [Work dir: /scratch/j_p3635_wFragPipe/outputFresh/j_p3635_wFragPipe]
/scratch/FragPipe14/philosopher database --annotate /scratch/j_p3635_wFragPipe/2020-10-26-decoys-reviewed-contam-UP000000589.fas --prefix rev

To Reproduce
It is the default LFQ-MBR workflow. I can share all you need.

Expected behavior
not throwing the error of ProteinProphet.

Please complete the following information:

• OS: Linux
• Version:
  Philosopher version: 3.3.11 (build 1601497354)

Additional context
This should only be the testrun before I want to excecute the workflow completely from commandline and then switching to the huge MetaproteomicsDB.

[prvst]

Hi @jjGG, this problem seems to be related to your system locale settings. I saw it happen before with systems that were not initially set to use English as their main language. Could you type and paste here the output of the following commands?

neofetch
and
locale

[jjGG]

Hello @prvst .. here the stdout.

jonas@fgcz-r-033:/scratch/j_p3635_wFragPipe/outputFresh/j_p3635_wFragPipe$ neofetch
-bash: neofetch: command not found
jonas@fgcz-r-033:/scratch/j_p3635_wFragPipe/outputFresh/j_p3635_wFragPipe$ locale
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
LANG=en_US.UTF-8
LANGUAGE=
LC_CTYPE=UTF-8
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=

best regards - jonas

[prvst]

Run the following command, then open a new terminal and run Philosopher one more time.

export LC_ALL=en_US.UTF-8

If it works, you can add the command to your .bash_rc file (or equivalent).

[jjGG]

Dear @prvst, I added the file to .bashrc but after logging in with another terminal it still would show the error.
But if I do the export before starting the fragPipeGUI it works like a charm now.

Thanks for the super response time.

Best regards and with this I close the issue

• jonas

[soymintc]

Just for the record, I had a similar error, and export LC_ALL=en_US.UTF-8 didn't work.
From EOSIO/eos#5586, I tried export LC_ALL="C", and philosopher proteinprophet worked like a charm 😁