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gtluu / timsconvert

https://gtluu.github.io/timsconvert/
Apache License 2.0
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Unable to Convert Bruker File Using Timsconvert Docker Version #64

Open rolivella opened 2 weeks ago

rolivella commented 2 weeks ago

Hello,

I'm encountering an issue when trying to convert a Bruker file using the Timsconvert Docker version. The process starts, but no output is generated.

Steps to Reproduce:

  1. I run the following Docker command:

    docker run --rm -v /home/proteomics/mydata/d/PRCRT-263/DDA/T061519_QC03_AurEl7_PM5_RA7_1_7694.d:/data proteomicsunitcrg/timsconvert:latest --input /data --outdir /data --verbose

  2. The following message appears in the console:

    INFO:root:2024-10-05T17:44:43.913204: Initialize Bruker .dll file...
INFO:root:2024-10-05T17:44:43.921000: Loading input data...

    However, nothing else happens after that.

  3. I checked the output folder, but no mzML files are created.

Folder Contents:

Here is the content of the input/output directory:

Input folder: /home/proteomics/mydata/d/PRCRT-263/DDA/T061519_QC03_AurEl7_PM5_RA7_1_7694.d

total 948576
4 -rw-r--r-- 1 root       root             127 oct  5 19:49 log_2024-10-05_17-49-57-314784.log
4 drwxr-xr-x 3 proteomics proteomics      4096 oct  5 19:49 .
4 -rw-r--r-- 1 root       root             127 oct  5 19:49 log_2024-10-05_17-49-27-913423.log
4 -rw-r--r-- 1 root       root             127 oct  5 19:47 log_2024-10-05_17-47-56-237279.log
4 -rw-r--r-- 1 root       root             127 oct  5 19:44 log_2024-10-05_17-44-57-991316.log
4 -rw-r--r-- 1 root       root             127 oct  5 19:44 log_2024-10-05_17-44-43-913094.log
4 drwxr-xr-x 4 proteomics proteomics      4096 oct  5 07:14 ..
4 drwxr-xr-x 3 proteomics proteomics      4096 oct  5 07:14 7694.m
164944 -rw-r--r-- 1 proteomics proteomics 168902656 may  3 16:45 analysis.tdf
774028 -rw-r--r-- 1 proteomics proteomics 792600576 may  3 16:45 analysis.tdf_bin
9552 -rw-r--r-- 1 proteomics proteomics   9778176 may  3 16:45 chromatography-data.sqlite
0 -rw-r--r-- 1 proteomics proteomics         0 may  3 16:45 chromatography-data.sqlite-journal
12 -rw-r--r-- 1 proteomics proteomics     10240 may  3 15:45 chromatography-data-pre.sqlite
8 -rw-r--r-- 1 proteomics proteomics      5314 may  3 15:45 SampleInfo.xml

Expected Behavior:

I expected the conversion process to complete successfully, generating mzML files in the output folder.

Actual Behavior:

The conversion process seems to hang after the initialization of the Bruker .dll file, and no mzML files are generated.

Any help or suggestions on how to resolve this would be appreciated. Thank you!

gtluu commented 1 week ago

Hi @rolivella, I see that you've made multiple attempts at the conversion. Would you be able to share one of the those *.log files either here or privately? Additionally, do you have any further information on this data (i.e. is this standard ddaPASEF data, how long was the acquisition, OS, etc.)?

rolivella commented 1 week ago

Thanks for your reply. Unfortunately, the data is not mine, but I can send you a link to access it privately if that helps. As for the logs, all of them contain the same information that I shared in my original post, which includes the following lines:

INFO:root:2024-10-05T17:44:43.913204: Initialize Bruker .dll file...
INFO:root:2024-10-05T17:44:43.921000: Loading input data...

Regarding the data, it is standard DDA-PASEF data, but I'm not sure of the exact acquisition duration. Please let me know how you'd like to proceed!

AnStaes commented 1 week ago

Hi all, It is standard DDA-PASEF and it was a 1h run!

Cheers, An

AnStaes commented 1 week ago

We never tried with the docker, but used it after installing conda...

gtluu commented 1 week ago

Hi @rolivella and @AnStaes I'm in the process of updating/testing the Docker container and nextflow workflow at the moment now that I've made a variety of updates to TIMSCONVERT's parameters and added support for iprm-PASEF MALDI workflows. Chances are I've missed something when it comes to updating the Docker containing which is why you are seeing TIMSCONVERT hang. Stay tuned for updates.

In the meantime, based on my testing the non-Docker CLI version should work, and I've also added a Qt based GUI that is still capable of batch conversion as well as of 2.0.0. Feel free to try those out in the meantime while I work on the nextflow update.

Lastly, @rolivella I see the mention regarding TIMSCONVERT and nf-core. Please let me know if there's anything else I can help with on that front.

rolivella commented 1 week ago

Thanks @gtluu for taking care of the Docker version of your software. We are very interested in the Docker container as we plan to add it to our Nextflow pipeline, avoiding the need to install additional software on the system.

Secondly, regarding the nf-core, I encourage you to develop the TIMSCONVERT module by following these instructions: nf-core module tutorial. Unfortunately, I don't have the time to work on it myself.

jonasscheid commented 1 week ago

Would be great to see timsconvert on Conda/Quay, then we could use it for conversion

AnStaes commented 1 week ago

Hi, . It is possible to run tims convert on conda! See image attached.

Cheers, An

On 11 Oct 2024 23:12, Jonas Scheid @.***> wrote:

Would be great to see timsconvert on Conda/Quay, then we could use it for conversion

— Reply to this email directly, view it on GitHubhttps://github.com/gtluu/timsconvert/issues/64#issuecomment-2408126411, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AG7GFS56VR6R2SMWXJGHKVDZ3A5MFAVCNFSM6AAAAABPNRFAEOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBYGEZDMNBRGE. You are receiving this because you were mentioned.Message ID: @.***>

leoschwarz commented 3 days ago

Hi all, this probably does not adress your original problem but for version 2.0.0 I had to install some libraries into the Docker container (or else even running with just --help raises an error).

I just took this snippet from https://forum.qt.io/topic/154450/build-a-docker-for-pyside6 which made it work for my use case:

RUN apt-get update && apt-get install -y \
    libgl1-mesa-glx \
    libxkbcommon-x11-0 \
    libxcb-icccm4 \
    libxcb-image0 \
    libxcb-keysyms1 \
    libxcb-randr0 \
    libxcb-render-util0 \
    libxcb-render0 \
    libxcb-shape0 \
    libxcb-sync1 \
    libxcb-xfixes0 \
    libxcb-xinerama0 \
    libxcb-xkb1 \
    libxcb1 \
    libxrender1 \
    libxi6 \
    libdbus-1-3 \
    libxcb-cursor0 \
    libegl1 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*