[SNK INFO] ERROR PIPELINE

[UrsulaOggenfuss]

Hi, first thank you for creating and providing this important tool!

I try to do the test run, but encounter several problems, and the error files are not helping me to really understand what went wrong (see attached file: tremolo_output.txt). I had to install TrEMOLO via conda, as I don't have sudo rights on my universities cluster. Additionally, I installed all needed tools with conda, and R packes in R, and added #include <stdio.h> to TrEMOLO/lib/C++/chain_to_id.cpp.

My problem seems similar to #4 , yet I already encounter warnings earlier, and my log only contains the error files Snakefile_insider.err and Snakefile_outside.err, with the error

Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
BrokenPipeError: [Errno 32] Broken pipe

I feel I'm missing something, and might have not installed a relevant tool, so I would really appreciate your input! Thank you very much! Ursula

[M-D75]

Hi,

Thank you for your feedback.

It seems that you have an old version of coreutils, the tee command does not find the -p option, which leads to an error:

tee: invalid option -- 'p'
Try 'tee --help' for more information.

TrEMOLO uses version 8.30, you can try this command:

conda install -c "conda-forge/label/gcc7" coreutils=8.30

an update of the documentation will be done to add this information.

if you have singularity already installed on your cluster, I can provide you with a link to download an already built container, so you can run it without being sudo, this will hopefully make it easier for you to launch the tool.

Mourdas

[chaopear]

Hi，Thank you very much for providing this tool. I'm having a similar problem, but since I built the environment myself, I'm not sure if there is a problem with my environment. Could you please send me the link to the built container, as I am not rooted. Thanks ! wang

[M-D75]

Hi,

Here is the download link (FileSender)

Mourdas

[chaopear]

Thank you very much! Wang

[M-D75]

You're welcome, I hope this helps.

I advise you to use at least version 3.6.0+ of singularity if you have a version higher or equal to that one installed on your cluster

Mourdas

[chaopear]

Thanks for reminding, my version is 3.11. Wang

[chaopear]

Thank you very much for providing the containers that have been built, it is indeed my own built environment that has the problem. Wang

[UrsulaOggenfuss]

Thank you very much for the help! I ended up with a different tool for this specific (small part of a ) project, yet I will consider TrEMOLO for a future bigger project. THank you very much for providing the tool and for the fast and helpful answer!

[M-D75]

Please, it's a pleasure to help you! I am delighted to hear that you have found a suitable solution for your current project. Thank you for your feedback.

Good luck with your projects !