FlashLFQ.FlashLFQEngine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures FATAL UNHANDLED EXCEPTION

[jj-umn]

I'm not sure if this is an error in my run of FlashLFQ or if this just happened to have an empty list.

(__flashlfq@0.1.102) galaxy@galaxy [~/tmp/test] % ln -s '/panfs/roc/risdb/galaxy/libdata/proteomics/UW/PASS00470/Mouse_XML/B6.PSMs.tsv' 'B6.PSMs.psmtsv' && mkdir spectrum_dir && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190425.dat' 'spectrum_dir/04-29-13_B6_Frac1_9uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190426.dat' 'spectrum_dir/04-29-13_B6_Frac2_9p5uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190427.dat' 'spectrum_dir/04-29-13_B6_Frac3_9p5uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190428.dat' 'spectrum_dir/04-29-13_B6_Frac4_8uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190429.dat' 'spectrum_dir/04-29-13_B6_Frac5_4uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190430.dat' 'spectrum_dir/04-29-13_B6_Frac6_5uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190431.dat' 'spectrum_dir/04-29-13_B6_Frac7_5uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190432.dat' 'spectrum_dir/04-29-13_B6_Frac8_9p5uL.mzML' && ln -s '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/190/dataset_190433.dat' 'spectrum_dir/04-29-13_B6_Frac9_9p5uL.mzML' && FlashLFQ --idt 'B6.PSMs.psmtsv' --rep spectrum_dir --ppm 10.0 --iso 5.0 --nis 2 --rmm true --mbr true --pau false && cat _FlashLFQ_Log.txt | sed 's/(Analysis summary for:).working./\1 /' > '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/196/dataset_196360.dat' && cp _FlashLFQ_QuantifiedBaseSequences.tsv '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/196/dataset_196362.dat' && cp _FlashLFQ_QuantifiedModifiedSequences.tsv '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/196/dataset_196363.dat' && cp _FlashLFQ_QuantifiedPeaks.tsv '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/196/dataset_196361.dat' && grep -v '^test$' _FlashLFQ_QuantifiedProteins.tsv > '/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/files/000/196/dataset_196364.dat' Opening PSM file B6.PSMs.psmtsv Done reading PSMs Setup is OK - running FlashLFQ engine Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac7_5uL Finding possible matched peptides for 04-29-13_B6_Frac7_5uL Checking errors Finished 04-29-13_B6_Frac7_5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac1_9uL Finding possible matched peptides for 04-29-13_B6_Frac1_9uL Checking errors Finished 04-29-13_B6_Frac1_9uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac3_9p5uL Finding possible matched peptides for 04-29-13_B6_Frac3_9p5uL Checking errors Finished 04-29-13_B6_Frac3_9p5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac4_8uL Finding possible matched peptides for 04-29-13_B6_Frac4_8uL Checking errors Finished 04-29-13_B6_Frac4_8uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac8_9p5uL Finding possible matched peptides for 04-29-13_B6_Frac8_9p5uL Checking errors Finished 04-29-13_B6_Frac8_9p5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac6_5uL Finding possible matched peptides for 04-29-13_B6_Frac6_5uL Checking errors Finished 04-29-13_B6_Frac6_5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac2_9p5uL Finding possible matched peptides for 04-29-13_B6_Frac2_9p5uL Checking errors Finished 04-29-13_B6_Frac2_9p5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac9_9p5uL Finding possible matched peptides for 04-29-13_B6_Frac9_9p5uL Checking errors Finished 04-29-13_B6_Frac9_9p5uL Assigning MS1 peaks to bins Quantifying peptides for 04-29-13_B6_Frac5_4uL Finding possible matched peptides for 04-29-13_B6_Frac5_4uL Checking errors Finished 04-29-13_B6_Frac5_4uL Running retention time calibration

Unhandled Exception: System.InvalidOperationException: Sequence contains no elements at System.Linq.Enumerable.Average (System.Collections.Generic.IEnumerable1[T] source) [0x0006a] in <5f01f5aacbb346938d6f9b4e69d4383a>:0 at FlashLFQ.FlashLFQEngine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures () [0x00436] in <e213ab8aae014a9999378ef2acd8f5fc>:0 at FlashLFQ.FlashLFQEngine.Run () [0x002cb] in <e213ab8aae014a9999378ef2acd8f5fc>:0 at FlashLFQExecutable.FlashLFQExecutable.Main (System.String[] args) [0x00547] in <5426307fba1e49e7a0c9affc907f11d0>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.InvalidOperationException: Sequence contains no elements at System.Linq.Enumerable.Average (System.Collections.Generic.IEnumerable1[T] source) [0x0006a] in <5f01f5aacbb346938d6f9b4e69d4383a>:0 at FlashLFQ.FlashLFQEngine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures () [0x00436] in :0 at FlashLFQ.FlashLFQEngine.Run () [0x002cb] in :0 at FlashLFQExecutable.FlashLFQExecutable.Main (System.String[] args) [0x00547] in <5426307fba1e49e7a0c9affc907f11d0>:0 (__flashlfq@0.1.102) galaxy@galaxy [~/tmp/test] %

[trishorts]

We'll have a look jj. Anything more that you could tell us about your run might help the debug.

[rmillikin]

Thanks - the error is specific enough that I can probably track it down. I'll check this out today and get back to you

[rmillikin]

I suspect I've found the problem; the retention time calibration tries to match common peaks between runs, but I'm guessing since your data is fractionated, there is at least one fraction that shares no peptides in common with one other file, resulting in the unintended crash. I think this should be fairly simple to resolve; are you able to share your files in the cloud? This would help me test my fix. You can email me the link (rmillikin at wisc dot edu). Thanks!

[rmillikin]

I think I've fixed this crash in 0.1.103; please let me know if it recurs. Apologies for the delay, we're putting out some fires in MetaMorpheus too.

[rmillikin]

I'm going to close this, feel free to reopen if you encounter the same problem (or open a new issue)