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From: Dickey, A. - A. <aar...@us...> - 2022-03-24 11:23:46
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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. |