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drop demo fails at rnaVariantCalling/pipeline/Snakefile line 446 #477
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This is directly trying to run the demo? Can you please try to run the following?
And see how it works? This is trying to build just this one file which should run everything up until that point |
Hi, yes this is just running I ran the command: and got the error:
I have attached the log but this file wasnt made today, it was dated 20/6/2023 |
First off, sorry I am unable to replicate your error with a fresh demo on my machine. It also seems like there is a typo? Is there a chance you didn't copy paste correct? No rule to produce /mnt/f/dropdemo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.tabl (if you use input functions make sure that they don't raise unexpected exceptions). Also looking at your log file it seems like there is a strange input error, maybe the data download got corrupted or altered by mistake. Can you please try to start fresh from a new demo directory? Or start looking through the rnaVariantCalling logs and see if the previous steps have good log files
You could also try (although I'm guessing this isn't the problem) to make sure your conda build is up to date. |
Many thanks for the suggestions. I have created a new demo dir and downloaded the demo files all ok. I ran `snakemake -c1 rnaVariantCalling' and get the error:
|
How does the previous log file look?
It's hard for me to recommend specific fixes since I can't replicate the problem myself. I'd guess there is some problem with the installation at some point. You could try to make sure that your conda environment is built correctly. We have a working yaml file for download, available here: https://www.cmm.in.tum.de/public/paper/drop_analysis/DROP_1.3.3.yaml You can then create a conda environment (called drop_env_133) by the following command
And subsequently retry the demo command using
I'm sorry you are having difficulty. |
Thanks for helping out as much as you can 👍 I will remake the env and see if anything crops up, i had problems with mamba so used conda, not sure if that created a problem.. Cheers |
One thing you can also try within that existing conda environment is just test if gatk is working properly. Run |
@nicholas-owen Any luck or updates on the installation? |
Hi! I wasnt sure if I should make this a new issue- If that is the case I will gladly open a new one! I seem to be having the same issue as nicholas-owen, but only with my own data. I called I called rule changeHeader: Waiting at most 360 seconds for missing files. I changed the latency time to 360 by adding Not sure what is going on. Thank you for your help, much appreciated! Best, Ali |
Can you please post the file Thanks |
The log exists but its empty! |
Can you try running just the changeHeader job?
|
Hi, I executed rule changeHeader: Waiting at most 5 seconds for missing files. Also-- Thanks for your quick replies! |
hmm, this is quite odd. Can you try to run the actual command of this step? You first run
Which should give you a command line script (although a long one). something like
Which you would copy paste and run independently of snakemake. You ideally should see a result like so:
|
@gaynora7 I think I have an idea of why your bam file is failing. It's probably because you don't have a readgroup named in the bam file. You can check by running the following:
You can check out this resource with links that may help you alleviate the problem (problem 2) |
@gaynora7 and @nicholas-owen I hope that this has been of some help, please let me know if you were able to get things working. Thanks |
Hi @nickhsmith, sorry for the delay in response! I really appreciate all the time you have spent looking into my issue. You are right, I don't have any readgroups in my bam files. I am looking into GATK Addorreplacereadgroups to address the issue. Thanks again, you have been super helpful! |
Hi @gaynora7 were you able to have a look at this and sort it out? |
HI, I am running
drop version 1.3.3
, with the command using demo data ofsnakemake --cores 1
but get the error:I have attached the log:
2023-06-20T223528.085086.snakemake.log
Thanks for looking into this.
Edit: I changed the latency wait to 120 and it didnt change the outcome.
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