analysis of DIA runs fails
Closed this issue · 4 comments
Description of the bug
I am trying to run quantms on a DIA dataset - acquired on an Exploris 480, with raw files converted to mzML.
I am using N E X T F L O W ~ version 23.10.0
with
-profile singularity
--acquisition_method dia
the option is recognized by nf, asI see the following promt:
`Input/output options
acquisition_method : dia`
The pipeline starts running and MZMLINDEXING is fine, but then the pipeline tries to run comet, rather then diann on those files, throwing the following error:
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET
- Load spectra: Warning - no spectra searched.
this happens on a CentOS 7 HPC environment, but also a Ubuntu 22.04.2 LTS (with -profile conda) with this files.
are there any additional parameters to consider for DIA data?
Command used and terminal output
No response
Relevant files
No response
System information
No response
Hi @jayieh Can you provide the full command you are using and also the configuration file SDRF.
hi, sure:
/home/j/jeirich/nextflow run nf-core/quantms --input '/cloud/wwu1/r_agfinkemeier/msdata/mito_hannover/design_DIA.sdrf' --database '/cloud/wwu1/r_agfinkemeier/msdata/mito_hannover/2023-10-18-decoys-contam-TAIR10__ARAPORT11_Editing_tragetP2.fasta' --outdir '/home/j/jeirich/mito_HN/quantms_res/DIA' -profile conda --decoy_string rev_ --max_cpus 16 --max_memory 16GB --max_time 17day --acquisition_method dia
(had to add a .txt, because as .sdrf github was refusing the ul...)
Hi @jayieh, Thanks for you using. Because the parameters are extracted from SDRF file when SDRF as input. you should add a column named comment[proteomics data acquisition method] in SDRF and fill it with NT=Data-Independent Acquisition;AC=PRIDE:0000450 value. There is a DIA example. The default value is DDA when the column is not in SDRF. The acquisition_method parameter will only take effect when experiment design file as input.
thanks for the quick reply! I will give it a try.