RNAseq sample upload bug

Flow App
1

Hi, I’m having some trouble with RNA-seq data upload. I’m uploading it from HPC Create at KCL, but get this error after first sample upload:

Traceback (most recent call last):
  File "/rds/prj/ppn_comp_analysis_rnp/users/luka.gnidovec/20241216_Flpin_3seq/flow_upload_3seq-DemuxSamples.py", line 24, in <module>
    sampleFlow = client.upload_sample(
  File "/users/k2371247/.local/lib/python3.9/site-packages/flowbio/upload.py", line 102, in upload_sample
    return self.sample(sample_id)
  File "/users/k2371247/.local/lib/python3.9/site-packages/flowbio/samples.py", line 13, in sample
    return self.execute(SAMPLE, variables={"id": id})["data"]["sample"]
  File "/users/k2371247/.local/lib/python3.9/site-packages/flowbio/client.py", line 27, in execute
    raise GraphQlError(resp["errors"])
flowbio.client.GraphQlError: [{'message': 'Cannot query field "type" on type "SampleType".', 'locations': [{'line': 3, 'column': 33}]}]

It does seem to upload the first sample’s read 1 to flow, but then it terminates.
In my upload code, I do specify the category as RNA-Seq. But on flow, the type of the uploaded read 1 is not set. Not sure if this is relevant or not.
Thanks in advance!
Luka

2

Hi Luka - could you try upgrading your flowbio python library with:

pip install --upgrade flowbio

There was a recent update to the library - the most recent version is 0.3.3.