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shuzhao-li-lab / asari

asari, metabolomics data preprocessing
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ValueError: max() arg is an empty sequence #85

Closed YuanyeChi closed 7 months ago

YuanyeChi commented 7 months ago 
Traceback (most recent call last):
  File "/usr/local/bin/asari", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/asari/main.py", line 182, in main
    process(parameters, args)
  File "/usr/local/lib/python3.10/site-packages/asari/main.py", line 48, in process
    __run_process__(parameters, args)
  File "/usr/local/lib/python3.10/site-packages/asari/main.py", line 45, in __run_process__
    process_project(list_input_files, parameters )
  File "/usr/local/lib/python3.10/site-packages/asari/workflow.py", line 84, in process_project
    EE = ext_Experiment(sample_registry, parameters)
  File "/usr/local/lib/python3.10/site-packages/asari/experiment.py", line 58, in __init__
    self.number_scans = self.get_max_scan_number(sample_registry)
  File "/usr/local/lib/python3.10/site-packages/asari/experiment.py", line 113, in get_max_scan_number
    return max([sample_registry[k]['max_scan_number'] for k in self.valid_sample_ids]) + 1
ValueError: max() arg is an empty sequence

with command

singularity exec --bind /projects/sh-li-lab/:/data /projects/sh-li-lab/share/YC/asari_amd_1.12.4.sif asari process --autoheight True --ppm 10 --mode pos --cores 24 -i "$subdir" -o "$output_path/asari" -j "ST000725_HILICpos_${subdir_name}_ppm5" | tee "$output_path/ST000725_HILICpos_${subdir_name}_ppm5.txt"

on some tof datasets

shuzhao-li commented 7 months ago

Looks like no valid sample.

YuanyeChi commented 7 months ago

Cool! I am retrieving and reproducing these error. If so, then I can just skip these datasets.

YuanyeChi commented 7 months ago 


Working on ~~ /projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos ~~ 

Estimating parameter for min peak_height based on  ['/projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_QC03.mzML', '/projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_SO061_SA074_1003cC1.mzML', '/projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_SO111_SA102_1007aC3.mzML']
Error in analyzing  /projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_QC03.mzML
Error in analyzing  /projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_SO061_SA074_1003cC1.mzML
Error in analyzing  /projects/sh-li-lab/public_data_mzml/metabolomics_workbench/ST000987/study/RPpos/GLA_CT_Lipids_SO111_SA102_1007aC3.mzML
Problems with input files: cannot convert float NaN to integer. Back to default min_peak_height.
shuzhao-li commented 7 months ago

We have not seen NaN in our data or other Orbi I think. Let's add a step to convert NaN to 0 for TOF.

YuanyeChi commented 7 months ago

Will do later today

YuanyeChi commented 7 months ago

The reason is pymzml cannot read mzML files from ST000987