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A cross-platform proteomics data analysis suite
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The setting was messed up and the spaces in the protein sequences of the fasta file broke IonQuant #1414

Closed martind2011 closed 8 months ago

martind2011 commented 8 months ago

log_2024-01-17_15-17-10.txt

fcyu commented 8 months ago

I think some settings were messed up. The search is a closed search, but somehow PTM-Shepherd was enabled to perform glycan assignment:

PTMShepherd [Work dir: D:\DRM\GluC_TS159_sDB]
java -Xmx204G -Dlibs.thermo.dir=D:\Users\fragpipe\tools\MSFragger-4.0\ext\thermo -cp D:\Users\fragpipe\tools\ptmshepherd-2.0.6.jar;D:\Users\fragpipe\tools\batmass-io-1.30.0.jar;D:\Users\fragpipe\tools\commons-math3-3.6.1.jar;D:\Users\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;D:\Users\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "D:\DRM\GluC_TS159_sDB\shepherd.config"

PTM-Shepherd version 2.0.6
(c) 2022 University of Michigan

Using Java 11.0.16.1 on 208896MB memory

Finding spectral data
    Indexing data from 1
    Indexing data from 10
    Indexing data from 2
    Indexing data from 3
    Indexing data from 4
    Indexing data from 5
    Indexing data from 6
    Indexing data from 7
    Indexing data from 8
    Indexing data from 9
Done finding spectral data

Caching spectral data
    Caching data from 1
        tims_23dec2213_Slot1-40_1_6907 - 7891 (101055 ms, 1214 ms)
    Done caching data from 1
    Caching data from 10
        tims_23dec2222_Slot1-49_1_6916 - 642 (31659 ms, 64 ms)
    Done caching data from 10
    Caching data from 2
        tims_23dec2214_Slot1-41_1_6908 - 6967 (92970 ms, 899 ms)
    Done caching data from 2
    Caching data from 3
        tims_23dec2215_Slot1-42_1_6909 - 2245 (47920 ms, 183 ms)
    Done caching data from 3
    Caching data from 4
        tims_23dec2216_Slot1-43_1_6910 - 2159 (43251 ms, 166 ms)
    Done caching data from 4
    Caching data from 5
        tims_23dec2217_Slot1-44_1_6911 - 3848 (70765 ms, 359 ms)
    Done caching data from 5
    Caching data from 6
        tims_23dec2218_Slot1-45_1_6912 - 1695 (79080 ms, 233 ms)
    Done caching data from 6
    Caching data from 7
        tims_23dec2219_Slot1-46_1_6913 - 1216 (43148 ms, 102 ms)
    Done caching data from 7
    Caching data from 8
        tims_23dec2220_Slot1-47_1_6914 - 744 (26285 ms, 53 ms)
    Done caching data from 8
    Caching data from 9
        tims_23dec2221_Slot1-48_1_6915 - 1230 (35483 ms, 92 ms)
    Done caching data from 9
Done caching spectral data

Counting MS2 scans for dataset 1
    7891 MS2 scans present in dataset 1
Done counting MS2 scans for dataset 1

Counting MS2 scans for dataset 10
    642 MS2 scans present in dataset 10
Done counting MS2 scans for dataset 10

Counting MS2 scans for dataset 2
    6967 MS2 scans present in dataset 2
Done counting MS2 scans for dataset 2

Counting MS2 scans for dataset 3
    2245 MS2 scans present in dataset 3
Done counting MS2 scans for dataset 3

Counting MS2 scans for dataset 4
    2159 MS2 scans present in dataset 4
Done counting MS2 scans for dataset 4

Counting MS2 scans for dataset 5
    3848 MS2 scans present in dataset 5
Done counting MS2 scans for dataset 5

Counting MS2 scans for dataset 6
    1695 MS2 scans present in dataset 6
Done counting MS2 scans for dataset 6

Counting MS2 scans for dataset 7
    1216 MS2 scans present in dataset 7
Done counting MS2 scans for dataset 7

Counting MS2 scans for dataset 8
    744 MS2 scans present in dataset 8
Done counting MS2 scans for dataset 8

Counting MS2 scans for dataset 9
    1230 MS2 scans present in dataset 9
Done counting MS2 scans for dataset 9

Creating combined histogram
    Generated histogram file for dataset 1 [-5 - 7]
    Generated histogram file for dataset 10 [-5 - 7]
    Generated histogram file for dataset 2 [-5 - 7]
    Generated histogram file for dataset 3 [-5 - 7]
    Generated histogram file for dataset 4 [-5 - 7]
    Generated histogram file for dataset 5 [-5 - 7]
    Generated histogram file for dataset 6 [-5 - 7]
    Generated histogram file for dataset 7 [-5 - 7]
    Generated histogram file for dataset 8 [-5 - 7]
    Generated histogram file for dataset 9 [-5 - 7]
Done creating combined histogram

Running peak picking
    Picked top 10 peaks
    Removed 3 peaks with insufficient PSMs
    Created summary table
Done running peak picking

Annotated summary table

Mapping modifications back into PSM lists

Created modification summary

Begin localization annotation
    tims_23dec2213_Slot1-40_1_6907 - 7891 lines (417 ms reading, 1314 ms processing)
    tims_23dec2222_Slot1-49_1_6916 - 642 lines (72 ms reading, 90 ms processing)
    tims_23dec2214_Slot1-41_1_6908 - 6967 lines (243 ms reading, 1005 ms processing)
    tims_23dec2215_Slot1-42_1_6909 - 2245 lines (91 ms reading, 346 ms processing)
    tims_23dec2216_Slot1-43_1_6910 - 2159 lines (82 ms reading, 256 ms processing)
    tims_23dec2217_Slot1-44_1_6911 - 3848 lines (125 ms reading, 521 ms processing)
    tims_23dec2218_Slot1-45_1_6912 - 1695 lines (79 ms reading, 218 ms processing)
    tims_23dec2219_Slot1-46_1_6913 - 1216 lines (72 ms reading, 153 ms processing)
    tims_23dec2220_Slot1-47_1_6914 - 744 lines (51 ms reading, 92 ms processing)
    tims_23dec2221_Slot1-48_1_6915 - 1230 lines (61 ms reading, 146 ms processing)
Done

Created localization reports

Begin similarity and retention time annotation
    Spectral data read into memory (235 ms reading)
    tims_23dec2213_Slot1-40_1_6907 - 7891 lines (542 ms processing)
    Spectral data read into memory (51 ms reading)
    tims_23dec2222_Slot1-49_1_6916 - 642 lines (20 ms processing)
    Spectral data read into memory (194 ms reading)
    tims_23dec2214_Slot1-41_1_6908 - 6967 lines (419 ms processing)
    Spectral data read into memory (92 ms reading)
    tims_23dec2215_Slot1-42_1_6909 - 2245 lines (113 ms processing)
    Spectral data read into memory (79 ms reading)
    tims_23dec2216_Slot1-43_1_6910 - 2159 lines (112 ms processing)
    Spectral data read into memory (123 ms reading)
    tims_23dec2217_Slot1-44_1_6911 - 3848 lines (182 ms processing)
    Spectral data read into memory (82 ms reading)
    tims_23dec2218_Slot1-45_1_6912 - 1695 lines (82 ms processing)
    Spectral data read into memory (82 ms reading)
    tims_23dec2219_Slot1-46_1_6913 - 1216 lines (53 ms processing)
    Spectral data read into memory (51 ms reading)
    tims_23dec2220_Slot1-47_1_6914 - 744 lines (41 ms processing)
    Spectral data read into memory (62 ms reading)
    tims_23dec2221_Slot1-48_1_6915 - 1230 lines (61 ms processing)
Done

Created similarity/RT reports

Combining and cleaning reports
Writing combined table for dataset 1
Writing combined table for dataset 10
Writing combined table for dataset 2
Writing combined table for dataset 3
Writing combined table for dataset 4
Writing combined table for dataset 5
Writing combined table for dataset 6
Writing combined table for dataset 7
Writing combined table for dataset 8
Writing combined table for dataset 9
Beginning glycan assignment
Glycan Assignment params:
    Glycan FDR: 1.0%
    Mass error (ppm): 50.0
    Isotope errors: [-1, 0, 1, 2, 3]
    Adducts: none
    Glycan Database size (including adducts): 1666
    mode: N-glycan
    Allowed Sites: N in N-X-S/T sequons only
    Y ion probability ratio: 5.0,0.50; dHex-containing: 2.0,0.50
    Oxonium probability ratios: NeuAc [2.0, 0.05, 0.2]; NeuGc [2.0, 0.05, 0.2]; dHex [2.0, 0.5, 0.1]; Phospho [2.0, 0.05, 0.2]; Sulfo [2.0, 0.1, 0.2]
Assigning glycans:
    tims_23dec2213_Slot1-40_1_6907 - 7891 (184 ms, 284 ms)
    tims_23dec2222_Slot1-49_1_6916 - 642 (40 ms, 21 ms)
    tims_23dec2214_Slot1-41_1_6908 - 6967 (166 ms, 79 ms)
    tims_23dec2215_Slot1-42_1_6909 - 2245 (43 ms, 38 ms)
    tims_23dec2216_Slot1-43_1_6910 - 2159 (49 ms, 31 ms)
    tims_23dec2217_Slot1-44_1_6911 - 3848 (133 ms, 71 ms)
    tims_23dec2218_Slot1-45_1_6912 - 1695 (51 ms, 31 ms)
    tims_23dec2219_Slot1-46_1_6913 - 1216 (33 ms, 30 ms)
    tims_23dec2220_Slot1-47_1_6914 - 744 (30 ms, 19 ms)
    tims_23dec2221_Slot1-48_1_6915 - 1230 (38 ms, 23 ms)
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Calculating Glycan FDR
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters
Created glyco reports
Done with glycan assignment
...

Then, it created a bunch of "non-existing" modifications to psm.tsv to confuse IonQuant. 

2024-01-17 15:17:07 [WARNING] - There are closed modifications: 1856.6556 and 1856.6557. Will keep 1856.6557
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 1872.6505 and 1872.6506. Will keep 1872.6506
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 1913.677 and 1913.6771. Will keep 1913.677
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2001.6931 and 2001.6932. Will keep 2001.6932
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2017.688 and 2017.6881. Will keep 2017.688
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2043.74 and 2043.7401. Will keep 2043.74
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2147.751 and 2147.7511. Will keep 2147.751
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2157.783 and 2157.7831. Will keep 2157.783
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2163.7459 and 2163.746. Will keep 2163.746
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2205.7928 and 2205.7929. Will keep 2205.7929
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2303.8409 and 2303.841. Will keep 2303.841
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2407.8518 and 2407.8519. Will keep 2407.8519
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2408.8722 and 2408.8723. Will keep 2408.8723
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2423.8467 and 2423.8468. Will keep 2423.8468
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2424.8671 and 2424.8672. Will keep 2424.8672
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2522.9152 and 2522.9153. Will keep 2522.9153
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2553.9097 and 2553.9098. Will keep 2553.9098
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2569.9046 and 2569.9047. Will keep 2569.9047
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2586.9199 and 2586.92. Will keep 2586.92
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2602.9148 and 2602.9149. Will keep 2602.9149
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2668.9731 and 2668.9732. Will keep 2668.9732
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2684.968 and 2684.9681. Will keep 2684.968
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2691.9513 and 2691.9514. Will keep 2691.9514
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2699.9676 and 2699.9677. Will keep 2699.9677
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2715.9625 and 2715.9626. Will keep 2715.9626
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2716.9829 and 2716.983. Will keep 2716.983
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2748.9727 and 2748.9728. Will keep 2748.9728
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2804.999 and 2804.9991. Will keep 2804.999
2024-01-17 15:17:07 [WARNING] - There are closed modifications: 2805.9943 and 2805.9944. Will keep 2805.9944
...

Since you had ptmshepherd.run-shepherd=false, I think the glycan assignment module was enabled to trigger PTMShepherd:

image

I have seen this issue many times and still don't know why

  1. The glycan assignment module will be enabled since users did not do that. Maybe it is enabled by default if there is no entry in the workflow files to disable it.
  2. even the PTM-Shepherd is enabled and performs the glycan assignment, it should not assign/create anything since it was a closed search. However, it creates a bunch of modifications.....

@dpolasky , could you take a look at the above two questions?

Could you please disable the Glycan assignment module if it is enabled, and re-rerun everything from scratch?

Best,

Fengchao

fcyu commented 8 months ago

Ah, yes, the Assign Glycans with FDR was set to true by default

https://github.com/Nesvilab/FragPipe/blob/5a098311c91eb711519835a109120c827e820d2a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/ptmshepherd/PTMSGlycanAssignPanel.java#L143

If users don't load the latest workflow to refresh the settings, it will be always enabled since there is no ptmshepherd.run_glyco_mode=false in the old workflow to disable it.

I also see another two with the same issue:

https://github.com/Nesvilab/FragPipe/blob/5a098311c91eb711519835a109120c827e820d2a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/ptmshepherd/PTMSGlycanAssignPanel.java#L249

https://github.com/Nesvilab/FragPipe/blob/5a098311c91eb711519835a109120c827e820d2a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/ptmshepherd/PTMSGlycanAssignPanel.java#L253

I will change them all to false since they should be disabled in most cases.

@dpolasky when adding new modules in the future, it would be better to set it to false by default unless that module will be used by most workflows.

So, the first question in my previous reply has been addressed, could you take a look at the second one?

Thanks,

Fengchao

dpolasky commented 8 months ago

@fcyu ahh, I see - yes will do in future.

For #2, the extra modifications are because the glycan database used needs to be passed to IonQuant, regardless of the MSFragger settings, since glycan assignment can override the mods used in MSFragger. Although it is unnecessary in this case because there are no glycans assigned. I think there are some ways to avoid this, but maybe we can discuss more internally - I was having some other issues with this setup recently.

Best, Dan

martind2011 commented 8 months ago

Thanks for the response! I did notice this as well and I am rerunning now. However, I have tried removing the assign glycan node already and I still get the same termination error. Here is the report from the search earlier without the glycan node.

-Dan log_2024-01-16_14-59-10.txt

fcyu commented 8 months ago

Thanks @dpolasky , so it appends those glycan modifications to the modmasses_ionquant.txt no matter if they are in the psm.tsv? Then, it explains everything. Yeah. let's discuss internally to make it better.

Best,

Fengchao

fcyu commented 8 months ago

Thanks for the response! I did notice this as well and I am rerunning now. However, I have tried removing the assign glycan node already and I still get the same termination error. Here is the report from the search earlier without the glycan node. log_2024-01-16_14-59-10.txt

@martind2011 Then, I have no clue about the error now. Could you share the fasta file and the .d folders with us? If yes, here is the link to upload the files https://www.dropbox.com/request/xl3yJ1cOVBwiw9bOj3KX

Thanks,

Fengchao

martind2011 commented 8 months ago

Sounds good,

The files are uploading now, these are Label-free GluC digests run on a timsTOF2 instrument.

-Dan

From: Fengchao @. Sent: Thursday, January 18, 2024 11:10 AM To: Nesvilab/FragPipe @.> Cc: Martin, Daniel @.>; Mention @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Ion Quant: errors creating tables. java.lang.NullPointerException (Issue #1414)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

Thanks for the response! I did notice this as well and I am rerunning now. However, I have tried removing the assign glycan node already and I still get the same termination error. Here is the report from the search earlier without the glycan node. log_2024-01-16_14-59-10.txthttps://github.com/Nesvilab/FragPipe/files/13978909/log_2024-01-16_14-59-10.txt

@martind2011https://github.com/martind2011 Then, I have no clue about the error now. Could you share the fasta file and the .d folders with us? If yes, here is the link to upload the files https://www.dropbox.com/request/xl3yJ1cOVBwiw9bOj3KXhttps://www.dropbox.com/request/xl3yJ1cOVBwiw9bOj3KX

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1414#issuecomment-1898781049, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFODTZ67RPNHPF5R33WDPTDYPFCNDAVCNFSM6AAAAABCAPA3FGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJYG44DCMBUHE. You are receiving this because you were mentioned.Message ID: @.***>

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fcyu commented 8 months ago

Hi @martind2011 , you uploaded the 2024-01-11-decoys-ADAMTS1_5_9_BGN_V1_V2_EQs.FASTA.fas.1.pepindex but could you also upload the 2024-01-11-decoys-ADAMTS1_5_9_BGN_V1_V2_EQs.FASTA.fas?

Thanks,

Fengchao

martind2011 commented 8 months ago

Sorry, it is attached.

-Dan

From: Fengchao @. Sent: Thursday, January 18, 2024 12:43 PM To: Nesvilab/FragPipe @.> Cc: Martin, Daniel @.>; Mention @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Ion Quant: errors creating tables. java.lang.NullPointerException (Issue #1414)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

Hi @martind2011https://github.com/martind2011 , you uploaded the 2024-01-11-decoys-ADAMTS1_5_9_BGN_V1_V2_EQs.FASTA.fas.1.pepindex but could you also upload the 2024-01-11-decoys-ADAMTS1_5_9_BGN_V1_V2_EQs.FASTA.fas?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1414#issuecomment-1898937575, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFODTZZJMRM5RIOXDX7CCWLYPFNL3AVCNFSM6AAAAABCAPA3FGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJYHEZTONJXGU. You are receiving this because you were mentioned.Message ID: @.***>

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Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

fcyu commented 8 months ago

@martind2011 Sorry, I did not see it. Could you upload the fasta file to the Dropbox link?

Thanks,

Fengchao

martind2011 commented 8 months ago

Just added it to the dropbox.

-Dan

From: Fengchao @. Sent: Thursday, January 18, 2024 1:59 PM To: Nesvilab/FragPipe @.> Cc: Martin, Daniel @.>; Mention @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Ion Quant: errors creating tables. java.lang.NullPointerException (Issue #1414)

https://github.com/martind2011

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

@martind2011 Sorry, I did not see it. Could you upload the fasta file to the Dropbox link?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1414#issuecomment-1899042020, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFODTZYTY2GGLV3QVDL4QA3YPFWGPAVCNFSM6AAAAABCAPA3FGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJZGA2DEMBSGA. You are receiving this because you were mentioned.Message ID: @.***>

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fcyu commented 8 months ago

@martind2011 FYI, there are no analysis.tdf_bin files in tims_23dec2214_Slot1-41_1_6908.d, tims_23dec2215_Slot1-42_1_6909.d, and tims_23dec2216_Slot1-43_1_6910.d. Since there are missing files, I will not try to reproduce your error. Let me know if you still want to and make sure that all necessary files have been uploaded.

Best,

Fengchao

martind2011 commented 8 months ago

Hello Fengchao,

I will try uploading them again from a different source, the upload may have been interrupted.

-Dan

From: Fengchao @. Sent: Friday, January 19, 2024 11:03 AM To: Nesvilab/FragPipe @.> Cc: Martin, Daniel @.>; Mention @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Ion Quant: errors creating tables. java.lang.NullPointerException (Issue #1414)

https://github.com/martind2011

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@martind2011 FYI, there are no analysis.tdf_bin files in tims_23dec2214_Slot1-41_1_6908.d, tims_23dec2215_Slot1-42_1_6909.d, and tims_23dec2216_Slot1-43_1_6910.d. Since there are missing files, I will not try to reproduce your error. Let me know if you still want to and make sure that all necessary files have been uploaded.

Best,

Fengchao

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fcyu commented 8 months ago

Thanks so much for the files. I have reproduced the error and located the cause. There are spaces in the protein sequences of your fasta file:

image

Those spaces made the program think the prev AA of the peptide FLSYPRFVE is blank, which crashed one function.

Best,

Fengchao

martind2011 commented 8 months ago

Awesome, perfect. I will make the fix, thank you!

-Dan

From: Fengchao @. Sent: Friday, January 19, 2024 3:21 PM To: Nesvilab/FragPipe @.> Cc: Martin, Daniel @.>; Mention @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Ion Quant: errors creating tables. java.lang.NullPointerException (Issue #1414)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

Thanks so much for the files. I have reproduced the error and located the cause. There are spaces in the protein sequences of your fasta file:

image.png (view on web)https://github.com/Nesvilab/FragPipe/assets/6926299/9675a66e-4ecd-405d-bc7c-0e7b2b41a25b

Those spaces made the program think the prev AA of the peptide FLSYPRFVE is blank, which crashed one function.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1414#issuecomment-1901057499, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFODTZZY4D7W6ZD4NLUPLNDYPLITLAVCNFSM6AAAAABCAPA3FGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBRGA2TONBZHE. You are receiving this because you were mentioned.Message ID: @.**@.>>

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Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.