Crux not supprting the PEFF file?

[JAVAN OKENDO]

Dear All,

I desperately need your help. I understand that comet supports the PEFF file format but when I run it through crux it gives the following error.

WARNING: Read parameter 'database_name' from parameter file, but is an argument, not an option.
WARNING: Read parameter 'peff_format' from parameter file, but no such parameter exists.
WARNING: Read parameter 'peff_obo' from parameter file, but no such parameter exists.
WARNING: Read parameter 'search_enzyme2_number' from parameter file, but no such parameter exists.
WARNING: Read parameter 'output_sqtstream' from parameter file, but no such parameter exists.
WARNING: Read parameter 'peptide_length_range' from parameter file, but no such parameter exists.
WARNING: Read parameter 'max_duplicate_proteins' from parameter file, but no such parameter exists.
WARNING: Read parameter 'equal_I_and_L' from parameter file, but no such parameter exists.
WARNING: Read parameter 'precursor_NL_ions' from parameter file, but no such parameter exists.
WARNING: The output directory '/cbio/users/javanokendo/BALF_

mgfFiles/cometSimproteoge' already exists.
Existing files will be overwritten.
WARNING: The file '/cbio/users/javanokendo/BALF_mgfFiles/cometSimproteoge/pipeline.log.txt' already exists and will be overwritten.
INFO: CPU: slurm-login
INFO: Crux version: 3.2-dcf56a2
INFO: Sat Mar 28 15:13:57 SAST 2020
INFO: Beginning pipeline.
INFO: Running pipeline with the following steps:
INFO: --> comet
INFO: --> percolator
INFO: Running comet...
INFO: Search will be run with the following files against database '/cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191111_C1_CH_T137P.mgf':
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180712_C0_CH_T035B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180712_C0_CH_T035BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180712_C0_CH_T090B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180712_C0_CH_T090BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180712_C0_CH_T090P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180731_C0_CH_T035P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180731_C0_CH_T043P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180731_C0_CH_T087B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180731_C0_CH_T087BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/180731_C0_CH_T087P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T136BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T136P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T137B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T160P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T163BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T164BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T165B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C1_CH_T165BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T136B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T137BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T142BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T142P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T160B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191025_C2_CH_T163B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191031_C1_CH_T160BCG.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191031_C1_CH_T164P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191031_C1_CH_T165P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191031_C3_CH_T163P.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191031_C3_CH_T164B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191104_C1_CH_T142B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191104_C3_CH_T043B1.mgf
INFO: --> /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/191104_C3_CH_T043BCG.mgf
FATAL: An exception occurred: Could not convert string '0.0'
./pipeline_crux.sh: line 15: 15457 Segmentation fault      (core dumped) $crux pipeline --search-engine comet --post-processor percolator --max-charge-feature 2 --spectral-counting-fdr 0.01 --estimation-method tdc --combine-charge-states F --auto-precursor-window warn --max-precursor-charge 5 --precursor-window 20 --precursor-window-type ppm --decoy_search 2 --peptide_mass_units 2 --mass_type_parent 1 --precursor_tolerance_type 1 --precursor_charge 2 --variable_mod01 15.9949 --add_C_cysteine 57.021464 --output-dir /cbio/users/javanokendo/BALF_mgfFiles/cometSimproteoge --parameter-file /cbio/users/javanokendo/cruxDataBaseworkflow/scrips/comet.params --overwrite T --spectrum-format mgf /cbio/users/javanokendo/BALF_mgfFiles/SIM_mgf/*.mgf

[Charles E Grant]

Hi Javan,

On Sunday, March 29, 2020 at 1:16:35 PM UTC-7, JAVAN OKENDO wrote:

Dear All,

I desperately need your help. I understand that comet supports the PEFF file format but when I run it through crux it gives the following error.

Support for PEFF was added to Comet in 2019. Crus is currently built using an earlier version of Comet that doesn't support PEFF. We are working on updating Crux to use the most recent version of Comet, but we haven't looked into the issue of PEFF support  yet. 

At the moment if you need PEFF support you'll have to use stand alone versions of Comet and Percolator.

[JAVAN OKENDO]

How cab I go about this percolator error? Do you have any idea as to why it happens?