Could not find LCMS file

[MKoesters]

Hi,

I'm trying to analyse the results I got from a msfragger open search.
Running batmass with Zero Peak calibration works fine, however I'd prefer PEP_ID calibration.
Specifying the search path with either the directory containing the raw, mzML and mgf file throws an error, as well as specifying one of these files directly.

This is the error I get:

12:43:24 INFO : Validating inputs
12:43:27 INFO : Total 1 found files in given paths without a regular expression to match against
12:43:27 INFO : Total 1 files supported by installed parsers
12:43:27 INFO : Loading 1 files
[parse ] /data/dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML
12:43:27 INFO : Filtering PSMs (rules follow):
Excluding delta mass range: [-0.5; 0.5]
Leaving only: Non-decoy PSMs
12:43:27 INFO : Parsing file: /data/dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML
12:43:28 WARN : Multiple SearchHits per SearchResult encountered. Only the first taken. File: /data/dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML
12:43:28 INFO : Sorted dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML by DELTA_MASS_ASCENDING
12:43:28 INFO : Writing cache: /data/dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML.deltamass-pep-cache
12:43:28 INFO : Building calibration for: dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML/dependent_search_20170505_exp0818_Puneet_WT-0h_01.mgf
12:43:28 ERROR: Could not find LCMS file ('dependent_search_20170505_exp0818_Puneet_WT-0h_01.mgf') for pep id file: dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML
12:43:28 ERROR: Could not update mass correction for: /data/dependent_search_20170505_exp0818_Puneet_WT-0h_01.pepXML
12:43:28 WARN : Try specifying Additional search paths for LCMS files. 'Search paths' text field in GUI, or '--search-path' command-line option.
12:43:28 ERROR: Error collecting input data, stopping

Can you tell me what I'm doing wrong?

Best,
Manuel

[jossmi]

I am also seeing this error. Wondering if this issue was fixed.

I supplied the Input path for the MSFragger search result and the path for the mzXML files, and chose the PEP_ID calibration option. Pasting log below.

Thanks,
Josh

12:57:41 INFO : Validating inputs
12:57:42 INFO : Total 25 found files in given paths without a regular expression to match against
12:57:42 INFO : Total 25 files supported by installed parsers
12:57:43 INFO : Loading 25 files
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1906_293T_proteinID_01A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1922_293T_proteinID_02A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1923_293T_proteinID_03A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1924_293T_proteinID_04A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1925_293T_proteinID_05A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1926_293T_proteinID_06A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1927_293T_proteinID_07A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1928_293T_proteinID_08A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1929_293T_proteinID_09A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1930_293T_proteinID_10A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1931_293T_proteinID_11A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1932_293T_proteinID_12A_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1937_293T_proteinID_01B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1938_293T_proteinID_02B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1939_293T_proteinID_03B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1940_293T_proteinID_04B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1941_293T_proteinID_05B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1942_293T_proteinID_06B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1943_293T_proteinID_07B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1944_293T_proteinID_08B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1945_293T_proteinID_09B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1946_293T_proteinID_10B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1947_293T_proteinID_11B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1948_293T_proteinID_12B_QE3_122212.pepXML
[cached] Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\interact.pep.xml
12:57:43 INFO : Filtering PSMs (rules follow):
Corrected delta mass: [-230.0; 500.0
Excluding delta mass range: [-0.5; 0.5]
Leaving only: Non-decoy PSMs
12:57:43 INFO : Cached file: Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1906_293T_proteinID_01A_QE3_122212.pepXML.deltamass-pep-cache
12:57:43 INFO : Building calibration for: b1906_293T_proteinID_01A_QE3_122212.pepXML/b1906_293T_proteinID_01A_QE3_122212mzXML
12:57:43 ERROR: Could not find LCMS file ('b1906_293T_proteinID_01A_QE3_122212mzXML') for pep id file: b1906_293T_proteinID_01A_QE3_122212.pepXML
12:57:43 ERROR: Could not update mass correction for: Z:\JS\Adductomics\PTMcruiser\Chick2015_Dataset\Report_fulldataset_CysFixedMod\b1906_293T_proteinID_01A_QE3_122212.pepXML
12:57:43 WARN : Try specifying Additional search paths for LCMS files. 'Search paths' text field in GUI, or '--search-path' command-line option.
12:57:43 ERROR: Error collecting input data, stopping

[jossmi]

For what it's worth, I noticed there is a missing period in the mzXML filenames it is looking for:

12:57:43 ERROR: Could not find LCMS file ('b1906_293T_proteinID_01A_QE3_122212mzXML') for pep id file: b1906_293T_proteinID_01A_QE3_122212.pepXML