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jonassibbesen / rpvg

Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
MIT License
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Errors while running rpvg #33

Closed prenderj closed 2 years ago

prenderj commented 2 years ago

Hi

I have been trying to run the rpvg example but unfortunately keep getting errors. If I compile from source or use the docker container with singularity I get this error:

$ ../../Progs/rpvg/bin/rpvg -t 4 -g graph.xg -p pantranscriptome.gbwt -f pantranscriptome.txt.gz -a mpmap_align.gamp -o rpvg --inference-model haplotype-transcripts
Running rpvg (commit: 0380bdb172bbe255a18ed070935fa0013dc02548)
Random number generator seed: 1646476787
terminate called after throwing an instance of 'std::runtime_error'
  what():  [io::ProtobufIterator] could not parse message
Aborted

If try to use the docker container directly I get this one:

$ docker run quay.io/jsibbesen/rpvg rpvg -t 4 -g graph.xg -p pantranscriptome.gbwt -f pantranscriptome.txt.gz -a mpmap_align.gamp -o rpvg --inference-model haplotype-transcripts
Running rpvg (commit: 0380bdb172bbe255a18ed070935fa0013dc02548)
Random number generator seed: 1646476861
rpvg: /home/rpvg/src/main.cpp:512: int main(int, char**): Assertion `frag_alignments_istream.is_open()' failed.

Any help would be great.

Thanks James

GeorgeBGM commented 2 years ago

Hi, James Can you give me some advice on how to install the software through the source code? I encountered a series of error messages, like this https://github.com/jonassibbesen/rpvg/issues/32. Thanks Du

GeorgeBGM commented 2 years ago

Hi, James

   Is there any progress on this issue?

   If I try to use the singularity container:
image 
  Besides, If I try to use the docker container with "-m" and "-d" option:
image

Thanks Du

jonassibbesen commented 2 years ago

Hi James and Du,

Thanks for writing. I am looking into this now. Will try to see if I can replicate the errors you shared.

Best,

Jonas

GeorgeBGM commented 2 years ago

Hi Jonas, I'm looking forward to your reply. by the way, are graph-based pan-genomic strategies will be extended to multi-omics analysis? Best, Du

jonassibbesen commented 2 years ago

Hi,

I am not able to replicate the error when using a compiled version of rpvg. I tried on both a mac and linux system. James, can you check that all the files are in the folder that you are running it from? This error could happen if rpvg can not find a file. I should probably add some more informative error messages if a file is not found.

I am, however, able to replicate the error with the docker container. I do not know what the issue is yet.

Best,

Jonas

prenderj commented 2 years ago

Hi Jonas

Thanks for getting back. I double checked was running in the right folder and seem to be:

image

I actually got the same error on two different computers.

jonassibbesen commented 2 years ago

I have recreated the docker container and it should now work. I am still not sure what happened with the old one. rpvg now completes on the example dataset without any problems:

docker run -it quay.io/jsibbesen/rpvg:latest
cd rpvg/example/
rpvg -t 4 -g graph.xg -p pantranscriptome.gbwt -f pantranscriptome.txt.gz -a mpmap_align.gamp -o rpvg --inference-model haplotype-transcripts
Running rpvg (commit: 0380bdb172bbe255a18ed070935fa0013dc02548)
Random number generator seed: 1647016967
Fragment length distribution parameters found in alignment (mean: 269.395, standard deviation: 44.4492)
Loaded graph, GBWT and r-index (0.958463 seconds, 1.09739 GB)
Fragment length distribution parameters re-estimated from alignment paths (location: 281.586, scale: 43.6241, shape: -0.167901)
Found alignment paths (5.32278 seconds, 1.09739 GB)
Clustered alignment paths (1.92169 seconds, 1.09739 GB)
Inferred path posterior probabilities and abundances (11.1969 seconds, 1.09739 GB)

Regarding your specific error James, I do not at the moment have any good ideas why this is happening. It has something to do with protobuf. What version of protobuf are you using?

prenderj commented 2 years ago

Hi Jonas

Thanks a lot. That is working for me now.

I think I may also have found the problem with the compiled version... I did a fresh install on AWS:

sudo apt install make cmake build-essential libz-dev protobuf-compiler libbz2-dev liblzma-dev libcurl4-openssl-dev pkg-config libjansson-dev

git clone --recursive https://github.com/jonassibbesen/rpvg.git
cd rpvg && mkdir build && cd build
cmake ..
make -j 2

And it worked and checking the input files they didn't match the size of the ones I had before, so sorry must have been an issue with these when copying them.

Thanks a lot for the help.