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pnnl / IonToolPack

A software tool for omics-agnostic automated quality control of mass spectrometry data.
BSD 2-Clause "Simplified" License
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I specifically don't understand why this error coming up. Using LFQ proteomics data #1

Open bioinformatic-guy opened 1 month ago

bioinformatic-guy commented 1 month ago

I'm using gui V1 on windows 11. Used paste MS runs from clipboard. to submit the raw file.

Error coming:

Converting raw files to mza format... Processing file: D:\GBC_2023\mzML\GBC_S2.mzML Processing file: D:\GBC_2023\mzML\GBC_S1.mzML Processing file: D:\GBC_2023\mzML\GBC_S3.mzML Traceback (most recent call last): File "mza.py", line 88, in File "mza.py", line 34, in write_mza File "source\MzML2mza.py", line 99, in write_mza_from_mzml File "h5py_hl\group.py", line 148, in create_dataset File "h5py_hl\dataset.py", line 137, in make_new_dset File "h5py_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5d.pyx", line 87, in h5py.h5d.create ValueError: Unable to create dataset (name already exists) [18984] Failed to execute script 'mza' due to unhandled exception! Closing remaining open files:D:\GBC_2023\mzML\new_folder\DataMza\GBC_S2_temp.mza...done Traceback (most recent call last): File "mza.py", line 88, in File "mza.py", line 34, in write_mza File "source\MzML2mza.py", line 99, in write_mza_from_mzml File "h5py_hl\group.py", line 148, in create_dataset File "h5py_hl\dataset.py", line 137, in make_new_dset File "h5py_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5d.pyx", line 87, in h5py.h5d.create ValueError: Unable to create dataset (name already exists) [19024] Failed to execute script 'mza' due to unhandled exception! Closing remaining open files:D:\GBC_2023\mzML\new_folder\DataMza\GBC_S1_temp.mza...done Traceback (most recent call last): File "mza.py", line 88, in File "mza.py", line 34, in write_mza File "source\MzML2mza.py", line 99, in write_mza_from_mzml File "h5py_hl\group.py", line 148, in create_dataset File "h5py_hl\dataset.py", line 137, in make_new_dset File "h5py_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5d.pyx", line 87, in h5py.h5d.create ValueError: Unable to create dataset (name already exists) [16920] Failed to execute script 'mza' due to unhandled exception! Closing remaining open files:D:\GBC_2023\mzML\new_folder\DataMza\GBC_S3_temp.mza...done

How to fix this issue, any idea?

aivett commented 1 month ago

Hello, Thank you for trying PeakQC! It seems that the 'id' of each spectrum in your mzML file is not unique. It could be that the run has multiple time segments. What was the original format before converting to mzML? Please would it be possible for you to share the mzML file so we can debug?