Conversion Error

[hjn0415a]

Hi, I successfully ran the test code.
but when I specify input and database, it doesn't work

nextflow run bigbio/quantms -r 1.3.0 -profile docker --input 'PXD001819.sdrf.tsv' --database '18Protein_SoCe_Tr_detergents_trace.fasta' --outdir .

[ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD001819.sdrf.tsv)'
duckdb.duckdb.ConversionException: Conversion Error: In Parquet reader of file "/usr/local/lib/python3.10/site-packages/sdrf_pipelines/ols/uberon.parquet":
failed to cast column "accession" from type VARCHAR to INTEGER: Could not convert string 'BFO:0000001' to INT32]

Which tsv and fasta files should I use for a test run?

[daichengxin]

Hi @hjn0415a, I can't reproduce your error in same parameters and files.

Could you try to enter this container or run it in conda env? Then we can try to find the file, so that we can figure out what happened.

[hjn0415a]

@daichengxin Thanks for your answer.
but I don't understand what this container is.
if I want to run it in conda env, do I just need to set up -profile conda?

[daichengxin]

Because you are running quantms in docker env. So you can try run docker ps -a to find out the container (nxf- prefix) from sdrf_pipelines module. Yes, you just set up -profile conda