Closed YuanyeChi closed 7 months ago
Looks like no valid sample.
Cool! I am retrieving and reproducing these error. If so, then I can just skip these datasets.
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.
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.
Will do later today
The reason is pymzml cannot read mzML files from ST000987
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