Metaproteomics module test execution problem

[MiguelCos]

Dear FragPipe team,

it was very interesting to see the implementation of a metaproteomics module in FragPipe.

We have a triple-organism dataset for which we would be interested to evaluate some kind of 'organims-specific' FDR calculation and I assumed something like this would be handled by this module.

Nevertheless, I got at error at the step of DbOptimizer execution. I attached the log file and also the error lines at the end here.

The fasta file I am using has a combination of EBI Uniprot sequences from Human, Arabidopsis and E. coli sequences + cRAP contaminants.

Sadly I didn't find any documentation regarding this beta module, I am sorry in case I wasn't thorough enough in my search for it.

Let me know if you need more information.

I'd like to know if this is an input or configuration error or simply a bug.

Best wishes,
Miguel

log_2025-11-12_16-20-35.txt

Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\1_programs\FragPipe-23.1\jre\bin\java.exe -cp C:\1_programs\FragPipe-23.1\lib\fragpipe-23.1.jar org.nesvilab.utils.FileDelete Z:\0_people\Heinrich\HUNTER_triple_mix_2025\January\preHUNTER\DIA\FP_23_1_test_metaproteomics_module\EX005864_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Metaproteomics [Work dir: Z:\0_people\Heinrich\HUNTER_triple_mix_2025\January\preHUNTER\DIA\FP_23_1_test_metaproteomics_module]
C:\1_programs\FragPipe-23.1\jre\bin\java.exe -Xmx194G -jar C:\1_programs\FragPipe-23.1\tools\metaproteomics\FP-Meta-1.0.1.jar DbOptimizer --projectDir Z:\0_people\Heinrich\HUNTER_triple_mix_2025\January\preHUNTER\DIA\FP_23_1_test_metaproteomics_module --fastaFile Z:\0_people\mcosenza\fastas_and_organims_annotations\fastas\ebi_reference_proteomes_uniprot_format\2025-11-10-decoys-h_sapiens_e_coli_a_thaliana_ebi_reference_one_sequence_per_gene_w_cRAP_2025_05.fasta.fas --outdir Z:\0_people\Heinrich\HUNTER_triple_mix_2025\January\preHUNTER\DIA\FP_23_1_test_metaproteomics_module --decoyTag rev_ --qvalue 0.01 --deltaHyperscore 0.0 --minPeptCntPerProt 1 --minUniqPeptCntPerProt 1 --minUniqPeptCnt 2 --taxonNameFile C:\1_programs\FragPipe-23.1\tools\metaproteomics\names.dmp --taxonNodeFile C:\1_programs\FragPipe-23.1\tools\metaproteomics\nodes.dmp --hostName "Homo sapiens" --iterations 3
2025-11-12 16:20:34 [INFO] - Executing DbOptimizer
2025-11-12 16:20:34 [INFO] - Constructing a taxonomy-informed database
2025-11-12 16:20:34 [INFO] - Loading PSM data
2025-11-12 16:20:34 [INFO] - Applying PSM filters
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.lang.Integer.intValue()" because the return value of "java.util.Map.get(Object)" is null
	at Input.MSFraggerPin.readSpectrumFile(MSFraggerPin.java:93)
	at Input.MSFraggerPin.<init>(MSFraggerPin.java:63)
	at Processor.ConsensusBuilder.run(ConsensusBuilder.java:89)
	at Processor.DbOptimizer.prepareData(DbOptimizer.java:164)
	at Processor.DbOptimizer.constructTaxonomyInformedDatabase(DbOptimizer.java:140)
	at Processor.DbOptimizer.process(DbOptimizer.java:43)
	at CMD.FragPipeMeta.runDbOptimizer(FragPipeMeta.java:158)
	at CMD.FragPipeMeta.lambda$initiate$2(FragPipeMeta.java:229)
	at Utility.Utility.estimateRuntime(Utility.java:81)
	at CMD.FragPipeMeta.initiate(FragPipeMeta.java:225)
	at CMD.FragPipeMeta.main(FragPipeMeta.java:275)
| FileName | # PSMs at Q-value 0.01 |
| -------- | ---------------------- |
| EX005860 | 12865                  |
| EX005861 | 14491                  |
| EX005862 | 13710                  |
| EX005863 | 14505                  |
| EX005859 | 13608                  |
| EX005864 | 13704                  |
Process 'Metaproteomics' finished, exit code: 1
Process returned non-zero exit code, stopping

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Cancelling 43 remaining tasks