Load In Errors For FragPipe And MaxQuant
=====================================================
Describe the Bug
The data load in functions are not working for me. I've tried with your example MQ data (both the txt and reformatted tsv) as well as my own dataset from FragPipe (DDA LFQ from v22.0). In all cases the "generate samplemap.tsv" function produces a blank box and doesn't make a file in the directory.
Logs
Error One: Failure to Make Samplemap
=== State Manager: Notifying Subscribers ===
Changed parameter: analysis_file
Value type: <class 'NoneType'>
Value: None
No subscribers registered
ERROR:bokeh.server.protocol_handler:error handling message
message: Message 'PATCH-DOC' content: {'events': [{'kind': 'MessageSent', 'msg_type': 'bokeh_event', 'msg_data': {'type': 'event', 'name': 'button_click', 'values': {'type': 'map', 'entries': [['model', {'id': 'p1074'}]]}}}]}
error: AttributeError("'NoneType' object has no attribute 'to_csv'")
Traceback (most recent call last):
File "bokeh\server\protocol_handler.py", line 94, in handle
File "bokeh\server\session.py", line 94, in _needs_document_lock_wrapper
File "bokeh\server\session.py", line 286, in _handle_patch
File "bokeh\protocol\messages\patch_doc.py", line 104, in apply_to_document
File "bokeh\document\callbacks.py", line 453, in invoke_with_curdoc
File "bokeh\protocol\messages\patch_doc.py", line 104, in <lambda>
File "bokeh\document\document.py", line 391, in apply_json_patch
File "bokeh\document\events.py", line 244, in handle_event
File "bokeh\document\events.py", line 279, in _handle_event
File "bokeh\document\callbacks.py", line 400, in trigger_event
File "bokeh\util\callback_manager.py", line 111, in _trigger_event
File "bokeh\document\callbacks.py", line 262, in notify_event
File "bokeh\document\callbacks.py", line 453, in invoke_with_curdoc
File "bokeh\util\callback_manager.py", line 107, in invoke
File "panel\reactive.py", line 580, in _server_event
File "panel\reactive.py", line 567, in _comm_event
File "panel\io\state.py", line 484, in _handle_exception
File "panel\reactive.py", line 565, in _comm_event
File "panel\reactive.py", line 502, in _process_bokeh_event
File "panel\widgets\button.py", line 241, in _process_event
File "param\parameterized.py", line 515, in _f
File "param\parameterized.py", line 517, in _f
File "param\parameters.py", line 541, in __set__
File "param\parameterized.py", line 517, in _f
File "param\parameterized.py", line 1564, in __set__
File "param\parameterized.py", line 2604, in _call_watcher
File "param\parameterized.py", line 2586, in _execute_watcher
File "alphaquant\ui\dashboard_parts_run_pipeline.py", line 1148, in _generate_samplemap
self.samplemap_table.value.to_csv(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'to_csv'
Error Two: Failure to Run Pipeline
=== Pipeline Parameters ===
input_file: C:\Users\XXXXX\Documents\local_work_folder\Tom_output_2025\combined_ion_mod.tsv
samplemap_df: DataFrame with 11 rows
samplemap_file: C:\Users\XXXX\Documents\local_work_folder\Tom_output_2025\results\samplemap.tsv
results_dir: C:\Users\XXXXXX\Documents\local_work_folder\Tom_output_2025\results
condpairs_list: None
modification_type: None
input_type_to_use: None
organism: human
min_num_ions: 1
minpep: 1
cluster_threshold_pval: 0.001
volcano_fdr: 0.05
volcano_fcthresh: 0.5
multicond_median_analysis: True
2025-03-13 12:37:42,862 - alphaquant.run_pipeline - INFO - Starting AlphaQuant
2025-03-13 12:37:42,921 - alphaquant.run_pipeline - INFO - Reformatted input file already exists. Using reformatted file of type fragpipe_precursors
2025-03-13 12:37:43,236 - root - ERROR - Error running pipeline: 'NoneType' object is not iterable
=== Pipeline Run Complete ===
Waiting for final progress checks...
Stopping progress monitor...
=== Checking Condition Progress ===
No condition progress dictionary, returning early
Progress monitor stopped successfully
Samplemap
<html xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=ProgId content=Excel.Sheet>
<meta name=Generator content="Microsoft Excel 15">
<link id=Main-File rel=Main-File
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip.htm">
<link rel=File-List
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip_filelist.xml">
<style>
<!--table
{mso-displayed-decimal-separator:"\.";
mso-displayed-thousand-separator:"\,";}
@page
{margin:.75in .7in .75in .7in;
mso-header-margin:.3in;
mso-footer-margin:.3in;}
tr
{mso-height-source:auto;}
col
{mso-width-source:auto;}
br
{mso-data-placement:same-cell;}
td
{padding-top:1px;
padding-right:1px;
padding-left:1px;
mso-ignore:padding;
color:black;
font-size:11.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:"Aptos Narrow", sans-serif;
mso-font-charset:0;
mso-number-format:General;
text-align:general;
vertical-align:bottom;
border:none;
mso-background-source:auto;
mso-pattern:auto;
mso-protection:locked visible;
white-space:nowrap;
mso-rotate:0;}
-->
</style>
</head>
<body link="#467886" vlink="#96607D">
sample | condition
-- | --
X_1kPa_1 | 1kPa
X_1kPa_2 | 1kPa
X_1kPa_3 | 1kPa
X_4kPa_1 | 4kPa
X_4kPa_2 | 4kPa
X_4kPa_3 | 4kPa
X_50kPa_1 | 50kPa
X_50kPa_2 | 50kPa
X_50kPa_3 | 50kPa
X_glass_1 | glass
X_glass_2 | glass
</body>
</html>
Head of Combined Ion Mod.tsv
<html xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=ProgId content=Excel.Sheet>
<meta name=Generator content="Microsoft Excel 15">
<link id=Main-File rel=Main-File
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip.htm">
<link rel=File-List
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip_filelist.xml">
<style>
<!--table
{mso-displayed-decimal-separator:"\.";
mso-displayed-thousand-separator:"\,";}
@page
{margin:.75in .7in .75in .7in;
mso-header-margin:.3in;
mso-footer-margin:.3in;}
tr
{mso-height-source:auto;}
col
{mso-width-source:auto;}
br
{mso-data-placement:same-cell;}
td
{padding-top:1px;
padding-right:1px;
padding-left:1px;
mso-ignore:padding;
color:black;
font-size:11.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:"Aptos Narrow", sans-serif;
mso-font-charset:0;
mso-number-format:General;
text-align:general;
vertical-align:bottom;
border:none;
mso-background-source:auto<br/>
# Load in Errors for FragPipe and MaxQuant: Q&A
=====================================================
## Q: What is the issue with the data load in functions?
A: The data load in functions are not working for me. I've tried with your example MQ data (both the txt and reformatted tsv) as well as my own dataset from FragPipe (DDA LFQ from v22.0). In all cases the "generate samplemap.tsv" function produces a blank box and doesn't make a file in the directory.
## Q: What is the error message I'm seeing?
A: The error message is:
```markdown
=== State Manager: Notifying Subscribers ===
Changed parameter: analysis_file
Value type: <class 'NoneType'>
Value: None
No subscribers registered
ERROR:bokeh.server.protocol_handler:error handling message
message: Message 'PATCH-DOC' content: {'events': [{'kind': 'MessageSent', 'msg_type': 'bokeh_event', 'msg_data': {'type': 'event', 'name': 'button_click', 'values': {'type': 'map', 'entries': [['model', {'id': 'p1074'}]]}}}]}
error: AttributeError("'NoneType' object has no attribute 'to_csv'")
Traceback (most recent call last):
File "bokeh\server\protocol_handler.py", line 94, in handle
File "bokeh\server\session.py", line 94, in _needs_document_lock_wrapper
File "bokeh\server\session.py", line 286, in _handle_patch
File "bokeh\protocol\messages\patch_doc.py", line 104, in apply_to_document
File "bokeh\document\callbacks.py", line 453, in invoke_with_curdoc
File "bokeh\protocol\messages\patch_doc.py", line 104, in <lambda>
File "bokeh\document\document.py", line 391, in apply_json_patch
File "bokeh\document\events.py", line 244, in handle_event
File "bokeh\document\events.py", line 279, in _handle_event
File "bokeh\document\callbacks.py", line 400, in trigger_event
File "bokeh\util\callback_manager.py", line 111, in _trigger_event
File "bokeh\document\callbacks.py", line 262, in notify_event
File "bokeh\document\callbacks.py", line 453, in invoke_with_curdoc
File "bokeh\util\callback_manager.py", line 107, in invoke
File "panel\reactive.py", line 580, in _server_event
File "panel\reactive.py", line 567, in _comm_event
File "panel\io\state.py", line 484, in _handle_exception
File "panel\reactive.py", line 565, in _comm_event
File "panel\reactive.py", line 502, in _process_bokeh_event
File "panel\widgets\button.py", line 241, in _process_event
File "param\parameterized.py", line 515, in _f
File "param\parameterized.py", line 517, in _f
File "param\parameters.py", line 541, in __set__
File "param\parameterized.py", line 517, in _f
File "param\parameterized.py", line 1564, in __set__
File "param\parameterized.py", line 2604, in _call_watcher
File "param\parameterized.py", line 2586, in _execute_watcher
File "alphaquant\ui\dashboard_parts_run_pipeline.py", line 1148, in _generate_samplemap
self.samplemap_table.value.to_csv(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'to_csv'
Q: What is the issue with the samplemap.tsv file?
A: The samplemap.tsv file is not being generated correctly. The "generate samplemap.tsv" function is producing a blank box and not making a file in the directory.
Q: What is the issue with the pipeline run?
A: The pipeline run is failing with the error message:
=== Pipeline Parameters ===
input_file: C:\Users\XXXXX\Documents\local_work_folder\Tom_output_2025\combined_ion_mod.tsv
samplemap_df: DataFrame with 11 rows
samplemap_file: C:\Users\XXXX\Documents\local_work_folder\Tom_output_2025\results\samplemap.tsv
results_dir: C:\Users\XXXXXX\Documents\local_work_folder\Tom_output_2025\results
condpairs_list: None
modification_type: None
input_type_to_use: None
organism: human
min_num_ions: 1
minpep: 1
cluster_threshold_pval: 0.001
volcano_fdr: 0.05
volcano_fcthresh: 0.5
multicond_median_analysis: True
2025-03-13 12:37:42,862 - alphaquant.run_pipeline - INFO - Starting AlphaQuant
2025-03-13 12:37:42,921 - alphaquant.run_pipeline - INFO - Reformatted input file already exists. Using reformatted file of type fragpipe_precursors
2025-03-13 12:37:43,236 - root - ERROR - Error running pipeline: 'NoneType' object is not iterable
=== Pipeline Run Complete ===
Waiting for final progress checks...
Stopping progress monitor...
=== Checking Condition Progress ===
No condition progress dictionary, returning early
Progress monitor stopped successfully
Q: What can I do to resolve the issue?
A: To resolve the issue, you can try the following:
- Check the samplemap.tsv file to ensure it is being generated correctly.
- Check the pipeline parameters to ensure they are set correctly.
- Check the input file to ensure it is in the correct format.
- Check the output directory to ensure it is writable.
- Try running the pipeline again with the same parameters.
Q: What is the version of the one-click installer I am using?
A: The version of the one-click installer you are using is Windows 64bit.
Q: What is the head of the combined ion mod.tsv file?
A: The head of the combined ion mod.tsv file is:
<html xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=ProgId content=Excel.Sheet>
<meta name=Generator content="Microsoft Excel 15">
<link id=Main-File rel=Main-File
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip.htm">
<link rel=File-List
href="file:///C:/Users/e76936hy/AppData/Local/Temp/msohtmlclip1/01/clip_filelist.xml">
<style>
<!--table
{mso-displayed-decimal-separator:"\.";
mso-displayed-thousand-separator:"\,";}
@page
{margin:.75in .7in .75in .7in;
mso-header-margin:.3in;
mso-footer-margin:.3in;}
tr
{mso-height-source:auto;}
col
{mso-width-source:auto;}
br
{mso-data-placement:same-cell;}
td
{padding-top:1px;
padding-right:1px;
padding-left:1px;
mso-ignore:padding;
color:black;
font-size:11.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:"Aptos Narrow", sans-serif;
mso-font-charset:0;
mso-number-format:General;
text-align:general;
vertical-align:bottom;
border:none;
mso-background-source:auto;
mso-pattern:auto;
mso-protection:locked visible;
white-space:nowrap;
mso-rotate:0;}
.xl63
{mso-number-format:Scientific;}
-->
</style>
</head>
<body link="#467886" vlink="#96607D">
Peptide Sequence | Modified Sequence | Prev AA | Next AA | Start | End | Peptide Length | M/Z | Charge | Compensation Voltage | Assigned Modifications | Protein | Protein ID | Entry Name | Gene | Protein Description | Mapped Genes | Mapped Proteins | X_1kPa_1 Spectral Count | X_1kPa_2 Spectral Count | X_1kPa_3 Spectral Count | X_4kPa_1 Spectral Count | X_4kPa_2 Spectral Count | X_4kPa_3 Spectral Count | X_50kPa_1 Spectral Count | X_50kPa_2 Spectral Count | X_50kPa_3 Spectral Count | X_glass_1 Spectral Count | X_glass_2 Spectral Count | X_1kPa_1 Apex Retention Time | X_1kPa_2 Apex Retention Time | X_1kPa_3 Apex Retention Time | X_4kPa_1 Apex Retention Time | X_4kPa_2 Apex Retention Time | X_4kPa_3 Apex Retention Time | X_50kPa_1 Apex Retention Time | X_