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Singularity yml parsing error #43
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This is odd indeed. I have found that line endings can sometimes get messed up when editing these files and it is hard to fix, but starting over is usually the solution. As a quick check, try to download the sample config file again with Let me know if not. There may be something else going on. Thanks. |
I just grabbed a fresh copy (curl -sL -o tephra_config.yml https://git.io/v5HFq) and tried running tephra without changes (so expecting it complain about missing files). Instead I got the same parsing error:
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This is what I get when I do the same:
Can you show what commands you ran to pull the image and start a container? For reference, I added a new entry to the config file in the last version and I'm thinking that is the issue. The way the YAML file is parsed it expects entries to be in a certain order, and that would cause issues with this config file and the previous Tephra version. |
Two commands to get the sif:
and then start it with:
the file stats: And the version of tephra: I pulled in a new copy today: And I'm seeing the same config error. |
That is the previous version. The latest is v0.12.5, so that is the issue. Let me make sure the latest version was pushed to Singularity Hub because that would be one explanation. |
Okay, running the commands should work now. It was my mistake. The latest image was pushed but I didn't realize you have to manually tag them as latest/default on the website, which is different than Docker. That is why running the 'pull' command was fetching the previous image. |
Thanks, that fixed the config issue. However, now I've got a different error (feel free to mark it as a separate issue):
I see three tephra_transposons_hmmdb* files, all size zero. In the yml file I have left tnradb and hmmdb default:
*Edit-- this seems to be same issue as #40 |
Okay, please share the output of |
correct, I am running on a cluster - I'm running qrsh to create an interactive session (qrsh -pe smp 12), then loading singularity, then the LC... command to start tephra.
and from hostnamectl
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I'm not sure what to do about the environment because I can't test that issue. I'm using the same singularity version and OS version, so the cluster environment seems to be the difference. I recommend trying the updated approach I added to the README file to start a container and load the ENV variables. If that does not work we can debug the environment variable list I suppose. |
I tried a couple of combinations of singularity shell with -C, but I'm still getting the same 'findltrs.pm line 142' error. These are the environmental variables once in singularity:
Perhaps I could specify the full path to the 'TephraDB' file that needs to be copied (though I'm not sure where that is)? |
Could you try the latest version (v0.13.0)? I would like to round up some old issues, particularly the container issues. |
Specifically, the same command you ran previously is working fine for me:
If this is no longer relevant, that is okay but let me know please and I'll close this issue. |
Sure, with the 0.13.0 version:
My focus is on other things currently, but I do hope to return to repeat finding in the Fall, so perhaps I can try some more in depth singularity checking then. Feel free to close this for housekeeping purposes.. |
Thanks for the response. I'll leave this issue open as a reminder. The Docker version and basic install or fine, but I do intend to understand and resolve these Singularity issues. |
I've downloaded tephra_latest.sif and I'm running it on singularity 3.3.0. When I try a small test I get an immediate error:
If I re-run the same command with no change to the config file I get a similar but different error:
Each time I run the command I can get a different error with the same config. I've only made a few changes to the default yml, and I've attached the file (with a .txt on the end) in case I've done something wrong in there. Any ideas on what is going wrong?
tephra_config.test1.yml.txt
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