What to expect after running installation and do you have any test data to check if it's working? #559
Replies: 12 comments 20 replies
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Hi @MauriAndresMU1313! |-- config
| |-- config.yaml
| |-- profiles
| | |-- desktop
| | `-- config.yaml
| | |-- slurm
| | `-- config.yaml
| |-- sample_sheet.csv
| `-- split_fasta.py
`-- workflow
`-- Snakefileincluding the configurations file |-- output_directory
| |-- data
| | |-- P01258.fasta
| | `-- P01579.fasta
| |-- features
| | |-- P01258_feature_metadata_2025-11-17.json.xz
| | |-- P01258.pkl.xz
| | |-- P01579_feature_metadata_2025-11-17.json.xz
| | `-- P01579.pkl.xz
| `-- predictions
| |-- P01258+P01579
| |-- ...
|-- slurm-logs
| |-- ...
| |-- reports
| `-- all_interfaces.csvPlease refer to https://github.com/KosinskiLab/AlphaPulldownSnakemake/tree/main and snakemake documentation for more details. |
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Thank you for provide that feedback! My bad for the basic questions... Now looks like is finally working, at least in the Click to expandI did not find similar error from another user, apparently this line is critical: Could you provide some feedback? Looks like is something related to Do you need that I provide more information? Thank you again for your feedback and help!! |
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Looking forward to your feedback @DimaMolod |
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Hi @MauriAndresMU1313 |
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Wow! Thank you for the quick response. So far I downloaded the latest containers, here you can see: All the process to obtain the container: Could you provide some feedback to know which container could be the source of the issue? Do you see something unusual? Do you need that I provide more details to make the process smoothly? Thank you again! |
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I do not know if related, but could be related to the differences on the tool selection in the following lines (selecting af2 and af3 for the following processes)? What do you think? |
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The problem is in this line: Yes, also please use either alphafold2 (everywhere), or alphafold3, depending on your needs |
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My bad! I did not realize about those details. Thank you for all the valuable feedback! @DimaMolod |
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Unfortunately, the process did not work completely. I edited the: This is the content: As you can see, I added the account, cpu and gpu partition names, and slurm-output-error (similar to the one of Then, I got the following error from I'm quite confuse here, I do not know how to continue, I did not find any similar on past issues.
Looking forward for your feedback! |
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Hi @MauriAndresMU1313 - slurm_account=a100v100
- slurm_output=slurm-logs/slurm_%j.out
- slurm_error=slurm-logs/slurm_%j.errHowever, the problem seems to be in permissions for your |
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Thank you for your quick response, I re-deployed and added the following lines in the default After running the I wonder, is not better to specify the partition on the terminal (with snakemake -argument1 ...) directly rather than the
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I forgot to mention, I removed the following lines from the Just in case |
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My apologies, I forgot to update one part in the |
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Well, unfortunately same issue: Permission looks fine: I checked more in deep the last So in fact, is completing some steps, however, failed for the permissions. UpdateI added the following argument to To check if changing the Let me know if you need that I share more details regarding config files, |
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No, ILP solver issue is expected and shouldn't cause an error. Your local rules are performed (files are downloaded from uniprot), but SLURM jobs fail. That likely means, that you have wrongly configured your slurm profile. You can try to submit your jobs manually with sbatch and see what is wrong. Sorry, I don't think I can help you any further at this stage, please consult with your local IT group. |
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Well, as you mentioned, I changed the default config file: Based on the last update, I'm checking with |
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I will come back with IT feedback, thank you for your time! |
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I'm in contact with IT team, hopefully I can come with some feedback. |
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Hi! Yes, it was one of our recent updates. Now all relevant directories are mounted automatically, so I wouldn't expect this to be a problem. I suspect that your SLURM settings are off, but let's see what the IT team going to say :-) |
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I hope you enjoyed the weekend! The permission was related to After checking the gpu model with the admin: I'm a quite confuse to be honest, I provided the model information, I tried with another partition and gpu model, I had the same issue. Removing the One of the comments of the admin was:
Looking forward for your feedback! Thank you again! @DimaMolod |
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Hi @MauriAndresMU1313 |
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Hi @DimaMolod, I work with @MauriAndresMU1313 on the HPC side. Our cluster expects the value for the This doesn't work in our cluster given that we use the Lua job submission plugin and SLURM expects to get just |
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Hi @burmek # SLURM resources
slurm_partition: "l4-1-gm24-c16-m64"
slurm_qos: "normal"
structure_inference_gpus_per_task: 1
# structure_inference_gpu_model: "l4" # <— remove or comment this out
structure_inference_tasks_per_gpu: 0In my understanding, with --gpus=1Sorry, I am at a conference now, but can have a deeper look starting from next week. |
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Thank you for your comment @burmek and feedback @DimaMolod! |
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Yes, you can do |
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Hi @DimaMolod, well I have some news, after adding last version, I was able to run the pipeline with one error, which is stoping me to have I'm checking what is the direct issue, I suspect that Thank you! |
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Hi! you just need to update your prediction container to the latest version. I recently renamed "alphafold" backend to "alphafold2", thus the error comes! Sorry for brevity, |
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Great, I updated the singularity image! Thank you for the quick reply! |
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Wow man! Finally...: Thank you for all the feedback! @DimaMolod |
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Huraay!! 🥳🥳 |
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Hi team!
I'm back with some questions, I while ago I asked for help to pull the
singularityimage or solving an issue withSLURM-srun.HPC policy obligate me to remove any data or libraries every 60 days, so in this case the last time that I installed this tool was more that 60 days, now I'm trying again, however, some changes were made compared with the last version.
So I followed all the steps:
STEP 1:
STEP 2:
Then, try to execute and see if is working:
In this case, only getting this output in the terminal:
and in the main directory I only have a new directory:
temp_fold(empty). I have the followingsingularityoutput in the terminal:Click to expand
If you are asking yourself, did I try the option (I did too):
After this point, I do not know how to continue, it's like something is missing, maybe some executable or files?
What am I missing?
Could you please provide some feedback?
How can I check if it's working?
Is it possible to provide an example of what to expect after the installation (showing how must look like the directory or the new files pulled)?
Looking forward to your feedback!
Thank you!
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