Closed jayieh closed 1 year ago
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.
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
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