07 Mar 2023 22:50:19,765 INFO : Copying experiment "Targeted Proteomics of Lung Squamous Cell Carcinomas" from folder /Moffitt Cancer Center - Koomen Lab/Moffitt_LSCC_Proteogenomics_Cohort_LC-MRM to /Panorama Public/2023/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM

07 Mar 2023 22:50:19,765 INFO : =======================================

07 Mar 2023 22:50:19,784 DEBUG: Resetting Job ID: 1aaf84eb-9faa-103b-8de3-fea6ddf5390e

07 Mar 2023 22:50:19,810 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

07 Mar 2023 22:50:19,810 INFO : 

07 Mar 2023 22:50:19,810 INFO : Exporting experiment.

07 Mar 2023 22:52:45,082 INFO : Exporting files metadata.

07 Mar 2023 22:52:45,082 DEBUG: [/Moffitt Cancer Center - Koomen Lab/Moffitt_LSCC_Proteogenomics_Cohort_LC-MRM]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export

07 Mar 2023 22:52:45,162 INFO : 

07 Mar 2023 22:52:45,162 INFO : Experiment export completed successfully.

07 Mar 2023 22:52:45,162 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

07 Mar 2023 22:52:45,192 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

07 Mar 2023 22:52:45,192 INFO : 

07 Mar 2023 22:52:45,192 INFO : Importing experiment.

07 Mar 2023 22:52:45,194 DEBUG: [/Panorama Public/2023/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export

07 Mar 2023 22:52:45,195 INFO : Loading folder properties (folder type, settings and active modules)

07 Mar 2023 22:52:45,196 DEBUG: [/Panorama Public/2023/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM] Folder type: Targeted MS

07 Mar 2023 22:52:45,196 DEBUG: [/Panorama Public/2023/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM] Active modules: Issues, API, TargetedMS, Pipeline, Assay, Experiment, MS2, Search, Query, Internal, Announcements, Wiki, FileContent, Core, PanoramaPublic

07 Mar 2023 22:52:45,301 INFO : Done importing folder properties (folder type, settings and active modules)

07 Mar 2023 22:52:45,302 INFO : Loading container specific module properties

07 Mar 2023 22:52:45,311 INFO : Done importing container specific module properties

07 Mar 2023 22:52:45,313 INFO : Loading etl definitions

07 Mar 2023 22:52:45,314 INFO : Loading wikis

07 Mar 2023 22:52:45,315 INFO : 0 wikis imported

07 Mar 2023 22:52:45,315 INFO : Done importing wikis

07 Mar 2023 22:52:45,315 INFO : Starting to copy files

07 Mar 2023 22:54:45,366 INFO : 122 files copied, now copying 09-08-2021_LSCCsamples-076.raw

07 Mar 2023 22:54:49,152 INFO : 125 files copied, now copying 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd

07 Mar 2023 22:54:51,898 INFO : 130 files copied, now copying 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd

07 Mar 2023 22:54:55,812 INFO : Copied 134 files

07 Mar 2023 22:54:55,812 INFO : Ensuring exp.data rows exist for imported files

07 Mar 2023 22:54:56,346 INFO : Starting Sample Type and Data Class import

07 Mar 2023 22:54:56,347 INFO : No types XAR file to process.

07 Mar 2023 22:54:56,347 INFO : Finished importing Sample Types and Data Classes

07 Mar 2023 22:54:56,348 INFO : Loading xar

07 Mar 2023 22:54:57,314 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip'

07 Mar 2023 22:54:57,316 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip.Core'

07 Mar 2023 22:54:57,317 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip.Output'

07 Mar 2023 22:54:57,317 DEBUG: Protocol import complete

07 Mar 2023 22:54:57,318 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11236:Moffitt_LSCC_Proteogenomics_Cohort_LC-MRM'

07 Mar 2023 22:54:57,318 DEBUG: Experiment/Run group import complete

07 Mar 2023 22:54:57,326 DEBUG: Protocol action set import complete

07 Mar 2023 22:54:57,334 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip'

07 Mar 2023 22:54:57,340 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11236:55d5b5c6-9e7c-103b-b327-fea6ddf5f3bc'

07 Mar 2023 22:54:57,343 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11236:55d5b590-9e7c-103b-b327-fea6ddf5f3bc'

07 Mar 2023 22:54:57,343 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip.Core'

07 Mar 2023 22:54:57,345 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11236:TargetedMS.ImportSkyZip.Output'

07 Mar 2023 22:54:57,345 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11236:55d5ba79-9e7c-103b-b327-fea6ddf5f3bc'

07 Mar 2023 22:54:57,346 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd into the system

07 Mar 2023 22:54:57,347 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd into the system

07 Mar 2023 22:54:57,347 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip into the system

07 Mar 2023 22:54:57,348 INFO : Starting import from 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip

07 Mar 2023 22:54:57,351 INFO : Starting to import Skyline document from 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip

07 Mar 2023 22:54:57,374 INFO : Expanding human_hcd_tryp_best.blib

07 Mar 2023 22:54:57,375 INFO : Expanding 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd

07 Mar 2023 22:54:57,931 INFO : Expanding 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.sky.view

07 Mar 2023 22:54:57,932 INFO : Expanding 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.sky

07 Mar 2023 22:54:58,050 INFO : Expanding 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyl

07 Mar 2023 22:54:58,195 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

07 Mar 2023 22:54:58,864 DEBUG: Starting to load chromatogram headers

07 Mar 2023 22:54:58,900 DEBUG: Done loading chromatogram headers

07 Mar 2023 22:54:59,111 INFO : Inserting sp|P62736|ACTA_HUMAN

07 Mar 2023 22:54:59,137 INFO : 1% Done

07 Mar 2023 22:54:59,363 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:54:59,364 INFO : Inserting sp|P60709|ACTB_HUMAN

07 Mar 2023 22:54:59,388 INFO : 2% Done

07 Mar 2023 22:54:59,631 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:54:59,632 INFO : Inserting sp|P02768|ALBU_HUMAN

07 Mar 2023 22:54:59,650 INFO : 3% Done

07 Mar 2023 22:54:59,815 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:54:59,815 INFO : Inserting sp|P10415|BCL2_HUMAN

07 Mar 2023 22:54:59,989 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:54:59,989 INFO : Inserting sp|O43521|B2L11_HUMAN

07 Mar 2023 22:55:00,012 INFO : 4% Done

07 Mar 2023 22:55:00,215 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:00,216 INFO : Inserting sp|Q7KYR7|BT2A1_HUMAN

07 Mar 2023 22:55:00,236 INFO : 5% Done

07 Mar 2023 22:55:00,408 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:00,409 INFO : Inserting sp|O00481|BT3A1_HUMAN

07 Mar 2023 22:55:00,551 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:00,551 INFO : Inserting sp|P04234|CD3D_HUMAN

07 Mar 2023 22:55:00,574 INFO : 6% Done

07 Mar 2023 22:55:00,783 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:00,783 INFO : Inserting sp|P07766|CD3E_HUMAN

07 Mar 2023 22:55:00,803 INFO : 7% Done

07 Mar 2023 22:55:00,927 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:00,927 INFO : Inserting sp|P01730|CD4_HUMAN

07 Mar 2023 22:55:01,113 INFO : 8% Done

07 Mar 2023 22:55:01,336 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:01,337 INFO : Inserting sp|P33681|CD80_HUMAN

07 Mar 2023 22:55:01,372 INFO : 9% Done

07 Mar 2023 22:55:01,497 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:01,497 INFO : Inserting sp|P42081|CD86_HUMAN

07 Mar 2023 22:55:01,619 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:01,619 INFO : Inserting sp|P01732|CD8A_HUMAN

07 Mar 2023 22:55:01,643 INFO : 10% Done

07 Mar 2023 22:55:01,792 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:01,792 INFO : Inserting sp|P24941|CDK2_HUMAN

07 Mar 2023 22:55:02,051 INFO : 11% Done

07 Mar 2023 22:55:02,260 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:02,260 INFO : Inserting sp|P11802|CDK4_HUMAN

07 Mar 2023 22:55:02,280 INFO : 12% Done

07 Mar 2023 22:55:02,445 INFO : 13% Done

07 Mar 2023 22:55:02,665 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:02,665 INFO : Inserting sp|Q00534|CDK6_HUMAN

07 Mar 2023 22:55:02,900 INFO : 14% Done

07 Mar 2023 22:55:03,086 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:03,086 INFO : Inserting sp|P42771|CDN2A_HUMAN

07 Mar 2023 22:55:03,105 INFO : 15% Done

07 Mar 2023 22:55:03,463 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:03,463 INFO : Inserting sp|O14757|CHK1_HUMAN

07 Mar 2023 22:55:03,482 INFO : 16% Done

07 Mar 2023 22:55:03,591 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:03,591 INFO : Inserting sp|O96017|CHK2_HUMAN

07 Mar 2023 22:55:03,715 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:03,715 INFO : Inserting sp|Q5H943|KKLC1_HUMAN

07 Mar 2023 22:55:03,735 INFO : 17% Done

07 Mar 2023 22:55:03,907 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:03,907 INFO : Inserting sp|P78358|CTG1B_HUMAN

07 Mar 2023 22:55:03,930 INFO : 18% Done

07 Mar 2023 22:55:04,057 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:04,057 INFO : Inserting sp|P35222|CTNB1_HUMAN

07 Mar 2023 22:55:04,283 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:04,283 INFO : Inserting sp|P17948|VGFR1_HUMAN

07 Mar 2023 22:55:04,311 INFO : 19% Done

07 Mar 2023 22:55:04,521 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:04,521 INFO : Inserting sp|P35916|VGFR3_HUMAN

07 Mar 2023 22:55:04,543 INFO : 20% Done

07 Mar 2023 22:55:04,715 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:04,715 INFO : Inserting sp|P04406|G3P_HUMAN

07 Mar 2023 22:55:04,750 INFO : 21% Done

07 Mar 2023 22:55:04,968 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:04,968 INFO : Inserting sp|P69905|HBA_HUMAN

07 Mar 2023 22:55:05,001 INFO : 22% Done

07 Mar 2023 22:55:05,210 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:05,210 INFO : Inserting sp|P68871|HBB_HUMAN

07 Mar 2023 22:55:05,444 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:05,444 INFO : Inserting sp|P01112|RASH_HUMAN

07 Mar 2023 22:55:05,466 INFO : 23% Done

07 Mar 2023 22:55:05,622 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:05,622 INFO : Inserting sp|Q14627|I13R2_HUMAN

07 Mar 2023 22:55:05,645 INFO : 24% Done

07 Mar 2023 22:55:05,828 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:05,829 INFO : Inserting sp|P35968|VGFR2_HUMAN

07 Mar 2023 22:55:06,058 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:06,058 INFO : Inserting sp|P10721|KIT_HUMAN

07 Mar 2023 22:55:06,077 INFO : 25% Done

07 Mar 2023 22:55:06,182 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:06,182 INFO : Inserting sp|P13647|K2C5_HUMAN

07 Mar 2023 22:55:06,379 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:06,379 INFO : Inserting sp|P02538|K2C6A_HUMAN

07 Mar 2023 22:55:06,588 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:06,588 INFO : Inserting sp|P08729|K2C7_HUMAN

07 Mar 2023 22:55:06,608 INFO : 26% Done

07 Mar 2023 22:55:06,781 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:06,781 INFO : Inserting sp|P02545|LMNA_HUMAN

07 Mar 2023 22:55:06,802 INFO : 27% Done

07 Mar 2023 22:55:07,159 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:07,159 INFO : Inserting sp|P43355|MAGA1_HUMAN

07 Mar 2023 22:55:07,196 INFO : 28% Done

07 Mar 2023 22:55:07,343 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:07,343 INFO : Inserting sp|P43363|MAGAA_HUMAN

07 Mar 2023 22:55:07,516 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:07,516 INFO : Inserting sp|P43357|MAGA3_HUMAN

07 Mar 2023 22:55:07,540 INFO : 29% Done

07 Mar 2023 22:55:07,697 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:07,697 INFO : Inserting sp|P43358|MAGA4_HUMAN

07 Mar 2023 22:55:07,875 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:07,875 INFO : Inserting sp|P43360|MAGA6_HUMAN

07 Mar 2023 22:55:07,905 INFO : 30% Done

07 Mar 2023 22:55:08,026 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,026 INFO : Inserting sp|O15479|MAGB2_HUMAN

07 Mar 2023 22:55:08,176 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,176 INFO : Inserting sp|O60732|MAGC1_HUMAN

07 Mar 2023 22:55:08,200 INFO : 31% Done

07 Mar 2023 22:55:08,329 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,329 INFO : Inserting sp|Q9UBF1|MAGC2_HUMAN

07 Mar 2023 22:55:08,360 INFO : 32% Done

07 Mar 2023 22:55:08,499 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,499 INFO : Inserting sp|P36507|MP2K2_HUMAN

07 Mar 2023 22:55:08,737 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,737 INFO : Inserting sp|P28482|MK01_HUMAN

07 Mar 2023 22:55:08,758 INFO : 33% Done

07 Mar 2023 22:55:08,937 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:08,937 INFO : Inserting sp|Q07820|MCL1_HUMAN

07 Mar 2023 22:55:08,964 INFO : 34% Done

07 Mar 2023 22:55:09,140 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:09,141 INFO : Inserting sp|Q29983|MICA_HUMAN

07 Mar 2023 22:55:09,292 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:09,293 INFO : Inserting sp|P46013|KI67_HUMAN

07 Mar 2023 22:55:09,317 INFO : 35% Done

07 Mar 2023 22:55:09,439 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:09,439 INFO : Inserting sp|P11836|CD20_HUMAN

07 Mar 2023 22:55:09,468 INFO : 36% Done

07 Mar 2023 22:55:09,699 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:09,699 INFO : Inserting sp|P01111|RASN_HUMAN

07 Mar 2023 22:55:09,913 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:09,913 INFO : Inserting sp|P09874|PARP1_HUMAN

07 Mar 2023 22:55:09,937 INFO : 37% Done

07 Mar 2023 22:55:10,156 INFO : 38% Done

07 Mar 2023 22:55:10,330 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:10,330 INFO : Inserting sp|Q9UGN5|PARP2_HUMAN

07 Mar 2023 22:55:10,484 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:10,484 INFO : Inserting sp|P12004|PCNA_HUMAN

07 Mar 2023 22:55:10,510 INFO : 39% Done

07 Mar 2023 22:55:10,689 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:10,689 INFO : Inserting sp|P16234|PGFRA_HUMAN

07 Mar 2023 22:55:10,715 INFO : 40% Done

07 Mar 2023 22:55:10,846 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:10,846 INFO : Inserting sp|P09619|PGFRB_HUMAN

07 Mar 2023 22:55:11,034 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:11,034 INFO : Inserting sp|P42336|PK3CA_HUMAN

07 Mar 2023 22:55:11,053 INFO : 41% Done

07 Mar 2023 22:55:11,242 INFO : 42% Done

07 Mar 2023 22:55:11,464 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:11,464 INFO : Inserting sp|O43653|PSCA_HUMAN

07 Mar 2023 22:55:11,630 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:11,631 INFO : Inserting sp|O95436|NPT2B_HUMAN

07 Mar 2023 22:55:11,655 INFO : 43% Done

07 Mar 2023 22:55:11,832 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:11,832 INFO : Inserting sp|Q15831|STK11_HUMAN

07 Mar 2023 22:55:11,854 INFO : 44% Done

07 Mar 2023 22:55:12,029 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:12,029 INFO : Inserting sp|P09758|TACD2_HUMAN

07 Mar 2023 22:55:12,283 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:12,283 INFO : Inserting sp|P24821|TENA_HUMAN

07 Mar 2023 22:55:12,306 INFO : 45% Done

07 Mar 2023 22:55:12,509 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:12,509 INFO : Inserting sp|O00220|TR10A_HUMAN

07 Mar 2023 22:55:12,530 INFO : 46% Done

07 Mar 2023 22:55:12,707 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:12,707 INFO : Inserting sp|O14763|TR10B_HUMAN

07 Mar 2023 22:55:12,827 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:12,827 INFO : Inserting sp|P07437|TBB5_HUMAN

07 Mar 2023 22:55:12,851 INFO : 47% Done

07 Mar 2023 22:55:13,044 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:13,044 INFO : Inserting sp|Q9H4B7|TBB1_HUMAN

07 Mar 2023 22:55:13,074 INFO : 48% Done

07 Mar 2023 22:55:13,482 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:13,483 INFO : Inserting sp|P08670|VIME_HUMAN

07 Mar 2023 22:55:13,507 INFO : 49% Done

07 Mar 2023 22:55:13,762 INFO : 50% Done

07 Mar 2023 22:55:13,985 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:13,985 INFO : Inserting sp|P30291|WEE1_HUMAN

07 Mar 2023 22:55:14,010 INFO : 51% Done

07 Mar 2023 22:55:14,133 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:14,133 INFO : Inserting KRAS Mutant

07 Mar 2023 22:55:14,342 INFO : 52% Done

07 Mar 2023 22:55:14,610 INFO : 54% Done

07 Mar 2023 22:55:14,963 DEBUG: Total peptides inserted: 3

07 Mar 2023 22:55:14,963 INFO : Inserting peptides1

07 Mar 2023 22:55:15,021 INFO : 55% Done

07 Mar 2023 22:55:15,371 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:15,371 INFO : Inserting sp|P31749|AKT1_HUMAN

07 Mar 2023 22:55:15,396 INFO : 56% Done

07 Mar 2023 22:55:15,571 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:15,571 INFO : Inserting sp|P31751|AKT2_HUMAN

07 Mar 2023 22:55:15,778 INFO : 57% Done

07 Mar 2023 22:55:15,942 INFO : 58% Done

07 Mar 2023 22:55:16,123 DEBUG: Total peptides inserted: 3

07 Mar 2023 22:55:16,123 INFO : Inserting sp|Q9Y243|AKT3_HUMAN

07 Mar 2023 22:55:16,272 INFO : 59% Done

07 Mar 2023 22:55:16,452 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:16,452 INFO : Inserting sp|P12830|CADH1_HUMAN

07 Mar 2023 22:55:16,630 INFO : 60% Done

07 Mar 2023 22:55:16,833 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:16,833 INFO : Inserting sp|P19022|CADH2_HUMAN

07 Mar 2023 22:55:16,855 INFO : 61% Done

07 Mar 2023 22:55:17,048 INFO : 62% Done

07 Mar 2023 22:55:17,151 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:17,151 INFO : Inserting sp|P00533|EGFR_HUMAN

07 Mar 2023 22:55:17,350 INFO : 63% Done

07 Mar 2023 22:55:17,520 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:17,520 INFO : Inserting sp|P04626|ERBB2_HUMAN

07 Mar 2023 22:55:17,541 INFO : 64% Done

07 Mar 2023 22:55:17,919 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:17,919 INFO : Inserting sp|P21860|ERBB3_HUMAN

07 Mar 2023 22:55:17,942 INFO : 65% Done

07 Mar 2023 22:55:18,169 INFO : 66% Done

07 Mar 2023 22:55:18,375 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:18,375 INFO : Inserting sp|Q02750|MP2K1_HUMAN

07 Mar 2023 22:55:18,398 INFO : 67% Done

07 Mar 2023 22:55:18,761 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:18,761 INFO : Inserting sp|P27361|MK03_HUMAN

07 Mar 2023 22:55:18,782 INFO : 68% Done

07 Mar 2023 22:55:18,998 INFO : 69% Done

07 Mar 2023 22:55:19,199 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:19,200 INFO : Inserting sp|P42345|MTOR_HUMAN

07 Mar 2023 22:55:19,440 INFO : 70% Done

07 Mar 2023 22:55:19,618 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:19,618 INFO : Inserting sp|P60484|PTEN_HUMAN

07 Mar 2023 22:55:19,642 INFO : 71% Done

07 Mar 2023 22:55:19,851 INFO : 72% Done

07 Mar 2023 22:55:20,027 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:20,027 INFO : Inserting sp|Q15116|PDCD1_HUMAN

07 Mar 2023 22:55:20,251 INFO : 73% Done

07 Mar 2023 22:55:20,422 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:20,422 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN

07 Mar 2023 22:55:20,448 INFO : 74% Done

07 Mar 2023 22:55:20,754 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:20,754 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN

07 Mar 2023 22:55:21,078 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:21,078 INFO : Inserting sp|Q9UM73|ALK_HUMAN

07 Mar 2023 22:55:21,104 INFO : 75% Done

07 Mar 2023 22:55:21,360 INFO : 76% Done

07 Mar 2023 22:55:21,613 INFO : 77% Done

07 Mar 2023 22:55:21,814 DEBUG: Total peptides inserted: 3

07 Mar 2023 22:55:21,814 INFO : Inserting sp|P30530|UFO_HUMAN

07 Mar 2023 22:55:21,833 INFO : 78% Done

07 Mar 2023 22:55:22,122 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:22,122 INFO : Inserting sp|P08581|MET_HUMAN

07 Mar 2023 22:55:22,141 INFO : 79% Done

07 Mar 2023 22:55:22,456 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:22,456 INFO : Inserting sp|P04629|NTRK1_HUMAN

07 Mar 2023 22:55:22,475 INFO : 80% Done

07 Mar 2023 22:55:22,691 INFO : 81% Done

07 Mar 2023 22:55:22,922 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:22,922 INFO : Inserting sp|Q16620|NTRK2_HUMAN

07 Mar 2023 22:55:22,939 INFO : 82% Done

07 Mar 2023 22:55:23,232 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:23,232 INFO : Inserting sp|Q16288|NTRK3_HUMAN

07 Mar 2023 22:55:23,247 INFO : 83% Done

07 Mar 2023 22:55:23,455 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:23,455 INFO : Inserting sp|P07949|RET_HUMAN

07 Mar 2023 22:55:23,469 INFO : 84% Done

07 Mar 2023 22:55:23,734 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:23,734 INFO : Inserting sp|P08922|ROS1_HUMAN

07 Mar 2023 22:55:23,759 INFO : 85% Done

07 Mar 2023 22:55:24,011 INFO : 86% Done

07 Mar 2023 22:55:24,179 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:24,179 INFO : Inserting sp|P16410|CTLA4_HUMAN

07 Mar 2023 22:55:24,196 INFO : 87% Done

07 Mar 2023 22:55:24,555 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:24,555 INFO : Inserting sp|P10398|ARAF_HUMAN

07 Mar 2023 22:55:24,570 INFO : 88% Done

07 Mar 2023 22:55:24,932 INFO : 89% Done

07 Mar 2023 22:55:25,158 DEBUG: Total peptides inserted: 3

07 Mar 2023 22:55:25,158 INFO : Inserting sp|P15056|BRAF_HUMAN

07 Mar 2023 22:55:25,176 INFO : 90% Done

07 Mar 2023 22:55:25,333 INFO : 91% Done

07 Mar 2023 22:55:25,527 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:25,527 INFO : Inserting sp|P04049|RAF1_HUMAN

07 Mar 2023 22:55:25,682 INFO : 92% Done

07 Mar 2023 22:55:25,956 DEBUG: Total peptides inserted: 3

07 Mar 2023 22:55:25,956 INFO : Inserting sp|P24385|CCND1_HUMAN

07 Mar 2023 22:55:25,979 INFO : 93% Done

07 Mar 2023 22:55:26,131 INFO : 94% Done

07 Mar 2023 22:55:26,256 DEBUG: Total peptides inserted: 2

07 Mar 2023 22:55:26,256 INFO : Inserting sp|P49841|GSK3B_HUMAN

07 Mar 2023 22:55:26,481 DEBUG: Total peptides inserted: 1

07 Mar 2023 22:55:26,481 INFO : Inserting Pierce RT Mix

07 Mar 2023 22:55:26,491 INFO : 95% Done

07 Mar 2023 22:55:26,662 INFO : 96% Done

07 Mar 2023 22:55:26,880 INFO : 97% Done

07 Mar 2023 22:55:27,115 INFO : 98% Done

07 Mar 2023 22:55:27,225 DEBUG: Total peptides inserted: 13

07 Mar 2023 22:55:27,227 INFO : Done parsing Skyline document.

07 Mar 2023 23:04:55,727 INFO : Creating and populating temp tables for Proportion values

07 Mar 2023 23:04:56,003 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

07 Mar 2023 23:04:57,247 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

07 Mar 2023 23:04:57,706 INFO : Cleaning up temp tables

07 Mar 2023 23:04:58,047 INFO : Completed import of Skyline document from 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip

07 Mar 2023 23:04:58,049 INFO : 100% Done

07 Mar 2023 23:04:58,053 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip into the system

07 Mar 2023 23:04:58,059 INFO : Done importing xar

07 Mar 2023 23:04:58,060 INFO : Loading pages and webpart properties

07 Mar 2023 23:04:58,146 INFO : Done importing 4 page(s) with 12 webpart(s)

07 Mar 2023 23:04:58,146 INFO : Loading File Browser config

07 Mar 2023 23:04:58,146 INFO : Done importing File Browser config

07 Mar 2023 23:04:58,147 INFO : Starting Sample Status Data import

07 Mar 2023 23:04:58,147 INFO : No sample types XAR file to process.

07 Mar 2023 23:04:58,147 INFO : Finished importing Sample Status Data

07 Mar 2023 23:04:58,152 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

07 Mar 2023 23:04:58,153 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping

07 Mar 2023 23:04:58,154 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping

07 Mar 2023 23:04:58,154 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping

07 Mar 2023 23:04:58,154 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

07 Mar 2023 23:04:58,155 INFO : Importing files metadata.

07 Mar 2023 23:04:58,155 DEBUG: [/Panorama Public/2023/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export

07 Mar 2023 23:04:58,155 INFO : 

07 Mar 2023 23:04:58,155 INFO : Experiment import completed successfully.

07 Mar 2023 23:04:58,155 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

07 Mar 2023 23:04:58,177 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

07 Mar 2023 23:04:58,177 INFO : 

07 Mar 2023 23:04:58,177 INFO : Checking for library folders.

07 Mar 2023 23:04:58,179 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

07 Mar 2023 23:04:58,194 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

07 Mar 2023 23:04:58,194 INFO : 

07 Mar 2023 23:04:58,194 INFO : Finishing up experiment copy.

07 Mar 2023 23:04:58,196 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

07 Mar 2023 23:04:58,196 INFO : Setting version on new experiment to 1

07 Mar 2023 23:04:58,196 INFO : Assigning a ProteomeXchange ID.

07 Mar 2023 23:04:58,318 INFO : Assigning a DOI.

07 Mar 2023 23:04:59,028 INFO : Assigned DOI: 10.6069/f553-kg47

07 Mar 2023 23:04:59,031 INFO : Updating access URL to point to the new copy of the data.

07 Mar 2023 23:04:59,035 INFO : Removing copy permissions given to Panorama Public

07 Mar 2023 23:04:59,046 INFO : Adding read permissions to all users that are folder admins in the source folder.

07 Mar 2023 23:04:59,053 INFO : Updating the 'Raw Data' tab configuration

07 Mar 2023 23:04:59,056 INFO : Updating dataFileUrls for run 10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip; targetedms run ID 154717

07 Mar 2023 23:04:59,057 INFO : Updating dataFileUrl...

07 Mar 2023 23:04:59,057 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip

07 Mar 2023 23:04:59,057 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM/@files/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03.sky.zip

07 Mar 2023 23:04:59,059 INFO : Updating dataFileUrl...

07 Mar 2023 23:04:59,059 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM_1aaf84d8-9faa-103b-8de3-fea6ddf5390e/_temp__2023-03-07_22-50-19/export/xar/experiments_and_runs.xar.exploded/Run152651/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd

07 Mar 2023 23:04:59,060 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Moffitt%20Cancer%20Center%20Koomen%20Lab%20-%20LSCC_Proteogenomics_Cohort_LC-MRM/@files/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL_2023-03-06_13-41-03/10-11-2021_LSCC_MRMassay_SCC-ID_NC-CALL.skyd

07 Mar 2023 23:04:59,069 INFO : Creating a reviewer account.

07 Mar 2023 23:04:59,266 INFO : Created reviewer with email: User panorama+reviewer175@proteinms.net

07 Mar 2023 23:04:59,275 INFO : Hiding the Data Pipeline tab.

07 Mar 2023 23:04:59,276 INFO : Updating Submission. Setting copiedExperimentId to 1592

07 Mar 2023 23:04:59,368 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'