thread panicked
Closed this issue · 3 comments
hi Michael
I have used searchGUI so far with great success for playing around with SAGE. I now want to move to Docker as no matter what I try with searchGUI the input file size seems to be restricted and I hope to circumvent this with a Docker container.
However, when I try to replicate my search of an Orbitrap DIA file, which works nicely in searchGUI, with the Docker I run into some problems:
I run Docker container via my Anaconda powershell
Config.json
(sage) PS C:\TMP_TIMSCONVERT\SAGE_Orbi_DIA> docker run -it --rm -v ${PWD}:/data ghcr.io/lazear/sage:master /app/sage -o /data /data/Config.json
[2024-02-22T20:29:12Z INFO sage] generated 60538165 fragments in 8925ms
thread 'thread '<unnamed>thread 'thread 'thread 'thread '<unnamed>' panicked at 'thread '<unnamed>thread '<unnamed><unnamed>thread '<unnamed>thread '' panicked at 'thread 'missing precursor information for MS2 scan, please check input files!<unnamed>' panicked at '<unnamed>' panicked at 'thread 'thread '<unnamed><unnamed>' panicked at '' panicked at '<unnamed>' panicked at '<unnamed>missing precursor information for MS2 scan, please check input files!<unnamed>thread '', <unnamed>' panicked at 'missing precursor information for MS2 scan, please check input files!' panicked at 'missing precursor information for MS2 scan, please check input files!' panicked at 'missing precursor information for MS2 scan, please check input files!missing precursor information for MS2 scan, please check input files!' panicked at 'missing precursor information for MS2 scan, please check input files!' panicked at '', ' panicked at '' panicked at 'src/spectrum.rsmissing precursor information for MS2 scan, please check input files!', missing precursor information for MS2 scan, please check input files!', missing precursor information for MS2 scan, please check input files!', missing precursor information for MS2 scan, please check input files!', missing precursor information for MS2 scan, please check input files!src/spectrum.rsmissing precursor information for MS2 scan, please check input files!missing precursor information for MS2 scan, please check input files!:', src/spectrum.rs', src/spectrum.rs', src/spectrum.rs', src/spectrum.rs', :', ', src/spectrum.rs220:src/spectrum.rs220:src/spectrum.rs:src/spectrum.rs:src/spectrum.rs220src/spectrum.rssrc/spectrum.rs:', :::220:220:220:::2201422014:220:thread '220:141414thread '220220:
:note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
:14::<unnamed>14' panicked at '
<unnamed>::1414220
14
missing precursor information for MS2 scan, please check input files!' p
anicked at '1414
:
', src/spectrum.rs:220:14
missing precursor information for MS2 scan, please check input files!
',
14src/spectrum.rssrc/spectrum.rs
::220220::1414
any idea what I am doing wrong here? It is the very first time using Docker, sorry to waste your time on this :(
Best, Klemens
The ghcr.io link is incorrect!
If I try:
$ docker run ghcr.io/lazear/sage /app/sage --version
> sage 0.4.0
I would try sage:latest 😀
(should also be easy to try the standalone binary, there are precompiled versions located here: https://github.com/lazear/sage/releases/tag/v0.14.6)?
hi Michael
I used the link provided in the documentation:
https://sage-docs.vercel.app/docs/started#run-via-docker
Would you generally recommend to always use latest, or just in this case?
It works perfectly with :latest
I downloaded the binaries and modified my system PATH, so I can now also directly run sage from command line. Thanks for the tip and you help!
Best, Klemens
Thanks for the catch, I have updated the docs.
I would recommend using the latest version, in case any bugs are uncovered. Sage has been pretty stable for a while though, so it's also OK to pin at v0.14 - all v0.14.* versions should produce identical results.
The next release in which either (a) results change, or (b) the JSON scheme undergoes a breaking change will be v0.15