"Tuple index out of range"

[hcadre]

Dear All,
trying to process the output of a FragPipe analysis (3 samples, 3 replicates each), I encountered a "tuple out of index" error, that abrogated the analysis pipeline (see below). This is with the filtering option for min. valid value set to 3 in at least one condition. When I require 3 valid values in both conditions (no missing values) then the analysis finishes without any further glitches. Any recommendations or ideas on how to proceed?
Best,
Hannes

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2025-06-11 16:56:21,560 - alphaquant.diffquant.condpair_analysis - INFO - checked 8500 of 8899 prots
2025-06-11 16:56:21,802 - alphaquant.diffquant.condpair_analysis - INFO - checked 8600 of 8899 prots
2025-06-11 16:56:22,008 - alphaquant.diffquant.condpair_analysis - INFO - checked 8700 of 8899 prots
2025-06-11 16:56:22,209 - alphaquant.diffquant.condpair_analysis - INFO - checked 8800 of 8899 prots
2025-06-11 16:56:22,359 - alphaquant.diffquant.condpair_analysis - INFO - start analysis of proteins w. completely missing values
numpy\core\fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
numpy\core_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
Traceback (most recent call last):
Traceback (most recent call last):
2025-06-11 16:56:22,609 - root - ERROR - Error running pipeline: tuple index out of range

=== Pipeline Run Complete ===
Waiting for final progress checks...
Stopping progress monitor...

=== Checking Condition Progress ===
Checking output folder: I:\exp_1170_1179_1183_1268_1284_1323\FragPipe23.0_20250603\alphaquant_results
Number of condition pairs to check: 3

Checking pair: 5.5_VS_4.5
Looking for file: I:\exp_1170_1179_1183_1268_1284_1323\FragPipe23.0_20250603\alphaquant_results\5.5_VS_4.5.results.tsv
File exists: True
Found result file for 5.5_VS_4.5

Checking pair: 6.5_VS_4.5
Looking for file: I:\exp_1170_1179_1183_1268_1284_1323\FragPipe23.0_20250603\alphaquant_results\6.5_VS_4.5.results.tsv
File exists: True
Found result file for 6.5_VS_4.5

Checking pair: 6.5_VS_5.5
Looking for file: I:\exp_1170_1179_1183_1268_1284_1323\FragPipe23.0_20250603\alphaquant_results\6.5_VS_5.5.results.tsv
File exists: True
Found result file for 6.5_VS_5.5

All conditions complete? True
Current overall status: ❌ Analysis Failed
=== Progress Check Complete ===

Progress monitor stopped successfully

[patrick-willems]

Hey, i have exactly the same error on a FragPipe ddaPASEF analysis.

[ammarcsj]

Hi Patrick and hcadre, thanks for the feedback! Would it be possible to share a minimal example file where this fails? It could be some issue with the file format that I need to adjust

[patrick-willems]

Hey,

I included the combined_ion.tsv here, as well with the samplemap.tsv and the log when running the command.

combined_ion.tsv

samplemap.tsv

log.txt