Closed jflucier closed 1 year ago
mwang87
commented
2 years ago Thanks for asking! I think those warnings are fine, we're likely doing a slightly wrong thing in writing out the mzML without the right units in that area, but intensity generally doesnt really need units anyway, but we'll take a look!
jflucier
commented
2 years ago Maybe of interest to you, here is me recipe file to build singularity container (your HPC users could be interested):
# build new image using this command:
# singularity build --force --fakeroot dia-ms.sif dia-ms.def
# test env:
# singularity exec --writable-tmpfs -e \
# dia-ms.sif \
# python /timsconvert/bin/run.py
BootStrap: docker
From: ubuntu:20.04
%setup
%environment
export PATH="/miniconda3/bin:$PATH"
%post
apt-get update && apt-get -y upgrade
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
apt-get -y install \
build-essential \
wget \
bzip2 \
ca-certificates \
git \
openjdk-17-jre \
cpanminus \
perl \
software-properties-common
rm -rf /var/lib/apt/lists/*
apt-get clean
cd /
wget -c https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
/bin/bash Miniconda3-py39_4.11.0-Linux-x86_64.sh -bfp /miniconda3
export PATH=/miniconda3/bin:$PATH
. /miniconda3/etc/profile.d/conda.sh
echo "__conda_setup="$('/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"" >> $SINGULARITY_ENVIRONMENT
echo "if [ $? -eq 0 ]; then" >> $SINGULARITY_ENVIRONMENT
echo " eval "$__conda_setup"" >> $SINGULARITY_ENVIRONMENT
echo "else" >> $SINGULARITY_ENVIRONMENT
echo " if [ -f \"/miniconda3/etc/profile.d/conda.sh\" ]; then" >> $SINGULARITY_ENVIRONMENT
echo " . \"/miniconda3/etc/profile.d/conda.sh\"" >> $SINGULARITY_ENVIRONMENT
echo " else" >> $SINGULARITY_ENVIRONMENT
echo " export PATH=\"/miniconda3/bin:$PATH\"" >> $SINGULARITY_ENVIRONMENT
echo " fi" >> $SINGULARITY_ENVIRONMENT
echo "fi" >> $SINGULARITY_ENVIRONMENT
echo "unset __conda_setup" >> $SINGULARITY_ENVIRONMENT
conda install -y python=3.7
conda install -y -c bioconda nextflow
cd /
git clone -c core.symlinks=true https://www.github.com/gtluu/timsconvert
cd /timsconvert
pip install -r requirements.txt
pip install git+https://github.com/gtluu/pyimzML
gtluu
commented
1 year ago Very late to this but to elaborate on the warning this issue mentions, that was an warning from an old version of psims (0.1.34) that appeared when no intensity value was explicitly provided for the base peak intensity. This resulted in the use of the default CV param MS:1000131 number of detector counts, which should be the correct CV param. 434d61f6696859074289a51f628a8c9677087c79 has updated psims to version 1.2.7 and explicitly calls for this CV param for base peak intensity value so this should no longer appear.
Also thank you for the singularity container, I will reference this as I (slowly) continue to add various recipe files.
Hi,
when I the program using the test data:
I get these warnings:
Here is the full exec log:
Is this normal behaviour or chould it be of concern?
tks