bigbio
Does not recognize file Uri
Description of the bug
I try to run quantms with a premade sdrf file, but it does not download the files using file uri. The download link works with wget, so I assume its the quantms not functioning as intended.
Config i use points to SDRF from https://github.com/bigbio/proteomics-sample-metadata/blob/8297770171ce449694d92a3df65d24fd327695b8/annotated-projects/PXD004683/PXD004683.sdrf.tsv#L2
executor > local (3)
[11/0c9362] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD004683.sdrf.tsv) [100%] 1 of 1, cached: 1 ✔
[88/82286b] BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING (PXD004683.sdrf.tsv) [100%] 1 of 1, cached: 1 ✔
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING -
[c1/3a7a77] BIG…:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (20150820_Haura-Pilot-TMT1-bRPLC02-1) [ 0%] 0 of 3
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS -
[0b/5cadda] BIGBIO_QUANTMS:QUANTMS:DECOYDATABASE (1) [100%] 1 of 1, cached: 1 ✔
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PSMCLEAN -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSMFDRCONTROL:IDSCORESWITCHER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSMFDRCONTROL:IDFILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATUREMAPPER:ISOBARICANALYZER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATUREMAPPER:IDMAPPER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FILEMERGE -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:IDFILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEINQUANT:IDCONFLICTRESOLVER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEINQUANT:PROTEINQUANTIFIER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEINQUANT:MSSTATSCONVERTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:MSSTATSTMT -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:EXTRACTPSMFEATURES -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PSMCLEAN -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMFDRCONTROL:IDSCORESWITCHER -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMFDRCONTROL:IDFILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:MSSTATS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:DIANNCFG -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:SILICOLIBRARYGENERATION -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_FINAL_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:DIANNSUMMARY -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:DIANNCONVERT -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:MSSTATS -
[- ] BIGBIO_QUANTMS:QUANTMS:SUMMARYPIPELINE -
ERROR ~ ERROR: Please check input file -> File Uri does not exist!
https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD004683/20150820_Haura-Pilot-TMT1-bRPLC07-2.raw
-- Check '.nextflow.log' file for details
Command used and terminal output
nextflow run bigbio/quantms -r 1.4.0 -profile singularity -c results/PXD004683/PXD004683_quantms.config -resume --outdir results/PXD004683/PXD004683_quantms_results --add_decoys
Relevant files
No response
System information
No response
Yes I noticed this as well. Yasset always recommends to download the files manually and set a root_folder. But definitely something to investigate.
Hi @MetteBoge , Did you see Staging foreign file: XXXXX prompt when running quantms? like this. I used similar command nextflow run main.nf -profile docker -resume --outdir PXD004683_quantms_results --input PXD004683_test.sdrf.tsv --database /home/daichengxin/gitrepo/latest/quantms/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta and quantms recognized file Uri
