Re: [proteowizard-support] [External Email] msconvert Singularity Error

[Dickey, A. - A. <aar...@us...>]

You’ve probably got a couple issues. The first is with singularity which is trying to create more than 50 bind mounts from your 1 raw file, yikes!. The second is with wine, which needs some additional info.

I’ve got an oldish msconvert singularity container (Sept, 2020 build, I think) that I use to convert Waters MSE raws. If you want to send me a link to your file, I can try your file with my container.

I can also send you some sample commands for building and running your own container or you can search the proteowizard archives for those.

To my knowledge, proteowizard only supports docker, not singularity.

Aaron

From: Tsvetkov, Nadia <nad...@ms...>
Date: Wednesday, March 23, 2022 at 3:33 PM
To: su...@pr... <su...@pr...>
Subject: [External Email][proteowizard-support] msconvert Singularity Error
[External Email]
If this message comes from an unexpected sender or references a vague/unexpected topic;
Use caution before clicking links or opening attachments.
Please send any concerns or suspicious messages to: Spa...@us...
Hello,

I am trying to convert .raw files into .mzML. I am trying do this on a Linux server. I do not have access to Docker, but instead I have Singularity (Singularity and Docker — Singularity container 2.5.1 documentation (singularity-user-docs.readthedocs.io)<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsingularity-user-docs.readthedocs.io%2Fen%2Flatest%2Fsingularity_and_docker.html&data=04%7C01%7C%7C0e3e8697e9394a0558bf08da0d0c56da%7Ced5b36e701ee4ebc867ee03cfa0d4697%7C0%7C0%7C637836643891451128%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=yrW3Zg1w%2FvVSNYr3uC%2FLkFpq1QSEpKp1z5DQU8%2BSglY%3D&reserved=0>)

I have successfully pulled the docker image (chambm/pwiz-skyline-i-agree-to-the-vendor-licenses - Docker Image | Docker Hub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhub.docker.com%2Fr%2Fchambm%2Fpwiz-skyline-i-agree-to-the-vendor-licenses&data=04%7C01%7C%7C0e3e8697e9394a0558bf08da0d0c56da%7Ced5b36e701ee4ebc867ee03cfa0d4697%7C0%7C0%7C637836643891451128%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=Y8SttFNnzu4%2F3kyUzzk7j5Rkaax%2B9Y4kYqmWiLdpj5s%3D&reserved=0>), but when I try to run the msconvert, I receive an error that tells me to contact su...@pr...<mailto:su...@pr...>.

Sincerely,

Nadia Tsvetkov

Bellow are the inputs/outputs
CentOS Linux 7 (Core)


[nadiats@login01 Nadia]$ singularity run docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /scratch/st-ljfoster-1/Nadia/ITB-10D-AL-1.raw
INFO:    Using cached SIF image
INFO:    Converting SIF file to temporary sandbox...
WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (83) bind mounts
format: mzML
    m/z: Compression-None, 64-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 64-bit
ByteOrder_LittleEndian
indexed="true"
outputPath: .
extension: .mzML
contactFilename:
runIndexSet:

spectrum list filters:

chromatogram list filters:

filenames:
  /scratch/st-ljfoster-1/Nadia\ITB-10D-AL-1.raw

processing file: /scratch/st-ljfoster-1/Nadia\ITB-10D-AL-1.raw
[C:\pwiz\msconvert.exe] Caught unknown exception.
Please report this error to su...@pr....
Attach the command output and this version information in your report:

ProteoWizard release: 3.0.21354 (9ee14c7)
Build date: Dec 20 2021 16:00:06
INFO:    Cleaning up image...
[nadiats@login01 Nadia]$ libgcc_s.so.1 must be installed for pthread_cancel to work
wine client error:18: write: Bad file descriptor
libgcc_s.so.1 must be installed for pthread_cancel to work
wine client error:18: write: Bad file descriptor
libgcc_s.so.1 must be installed for pthread_cancel to work
wine client error:18: write: Bad file descriptor
wineserver: could not save registry branch to system.reg : No such file or directory




This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.