mamba installation problem

[gaworj]

Hi,

Thank you for wonderful assembly pipeline!

I have successfully installed dragonflye via mamba but unfortunately installed v1.0.7.

So I decided to force mamba to install newest version:

mamba create -n dragonflye -c conda-forge -c bioconda dragonflye=1.0.13

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    mamba (0.22.1) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack

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WARNING: A conda environment already exists at '/home/jang/anaconda3/envs/mamba/envs/dragonflye' Remove existing environment (y/[n])? y

Looking for: ['dragonflye=1.0.13']

conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache r/linux-64 Using cache r/noarch Using cache pkgs/main/noarch No change pkgs/r/noarch No change pkgs/r/linux-64 No change pkgs/main/linux-64 No change cruizperez/linux-64 No change cruizperez/noarch No change Encountered problems while solving:

• nothing provides cudatoolkit 8.0.* needed by tensorflow-gpu-base-1.4.1-py27h01caf0a_0

Any hints?

I would like to run dragonflye with medaka using gpu or cpu and finally polish the assembly with polypolish.

Can you also add --prefix option for dragonflye to set custom file name for the final assembly?

Bests, Jan

[rpetit3]

I just tried and it worked. I am however using Miniconda. I've attached an environment export to try if you want.

Otherwise, does anything change if you also pin tensorflow-gpu?

mamba create -n dragonflye -c conda-forge -c bioconda 'dragonflye=1.0.13' 'tensorflow-gpu>=2.*'

dragonflye-env.txt

[gaworj]

I have followed your suggestion:

mamba create -n dragonflye -c conda-forge -c bioconda 'dragonflye=1.0.13' 'tensorflow-gpu>=2.*'

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             /  \  /  \  /  \  /  \
            /    \/    \/    \/    \

███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / _/ _/ _/ \ o _, / _/ ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

    mamba (0.22.1) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['dragonflye=1.0.13', "tensorflow-gpu[version='>=2.*']"]

r/linux-64 No change bioconda/noarch 3.7MB @ 3.2MB/s 1.2s pkgs/main/linux-64 No change conda-forge/noarch 9.5MB @ 4.8MB/s 2.1s pkgs/r/noarch No change r/noarch No change pkgs/r/linux-64 No change pkgs/main/noarch No change cruizperez/linux-64 No change bioconda/linux-64 4.4MB @ 1.2MB/s 3.6s conda-forge/linux-64 25.8MB @ 4.1MB/s 6.8s cruizperez/noarch No change Encountered problems while solving:

• package tensorflow-gpu-2.0.0-h0d30ee6_0 requires tensorflow 2.0.0, but none of the providers can be installed

Second option:

conda create -n dragonflye --file dragonflye.txt

CondaValueError: could not parse 'name: dragonflye' in: dragonflye.txt

..?

[rpetit3]

Try this: conda env create -f dragonflye.txt

[gaworj]

File extension format was wrong:

conda env create -f dragonflye.yml

Installation in progress...

[rpetit3]

Apologies, should have mention filename change was needed. GitHub doesn't all yaml files to be uploaded

[gaworj]

OK, so now I have correct dragonflye version but encopuntered medaka issue:

[polishing - medaka (1 of 2)] Running medaka consensus [polishing - medaka (1 of 2)] [18:46:50 - Predict] Reducing threads to 2, anymore is a waste. [polishing - medaka (1 of 2)] [18:46:50 - Predict] Setting tensorflow inter/intra-op threads to 2/1. [polishing - medaka (1 of 2)] [18:46:50 - Predict] Processing region(s): contig_1:0-2039123 contig_2:0-19600 contig_3:0-18712 [polishing - medaka (1 of 2)] [18:46:50 - Predict] Using model: /home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/medaka/data/r941_min_sup_g507_model.tar.gz. [polishing - medaka (1 of 2)] [18:46:50 - Predict] Found a GPU. [polishing - medaka (1 of 2)] [18:46:50 - Predict] If cuDNN errors are observed, try setting the environment variable TF_FORCE_GPU_ALLOW_GROWTH=true. To explicitely disable use of cuDNN use the commandline option `--disable_cudnn. If OOM (out of memory) errors are found please reduce batch size. [polishing - medaka (1 of 2)] [18:46:50 - Predict] Processing 5 long region(s) with batching. [polishing - medaka (1 of 2)] [18:46:50 - ModelLoad] GPU available: building model with cudnn optimization [polishing - medaka (1 of 2)] [18:46:50 - MdlStrTF] ModelStoreTF exception <class 'tensorflow.python.framework.errors_impl.InternalError'> [polishing - medaka (1 of 2)] Traceback (most recent call last): [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/bin/medaka", line 11, in [polishing - medaka (1 of 2)] sys.exit(main()) [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/medaka/medaka.py", line 720, in main [polishing - medaka (1 of 2)] args.func(args) [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/medaka/prediction.py", line 160, in predict [polishing - medaka (1 of 2)] model = model_store.load_model(time_steps=args.chunk_len) [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/medaka/datastore.py", line 159, in load_model [polishing - medaka (1 of 2)] self.model = model_partial_function(time_steps=time_steps) [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/medaka/models.py", line 144, in build_model [polishing - medaka (1 of 2)] gru = GRU( [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/tensorflow/python/keras/layers/recurrent_v2.py", line 379, in init [polishing - medaka (1 of 2)] if context.num_gpus() > 0: [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/tensorflow/python/eager/context.py", line 2046, in num_gpus [polishing - medaka (1 of 2)] return context().num_gpus() [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/tensorflow/python/eager/context.py", line 1047, in num_gpus [polishing - medaka (1 of 2)] self.ensure_initialized() [polishing - medaka (1 of 2)] File "/home/jang/anaconda3/envs/mamba/envs/dragonflye/lib/python3.8/site-packages/tensorflow/python/eager/context.py", line 515, in ensure_initialized [polishing - medaka (1 of 2)] context_handle = pywrap_tfe.TFE_NewContext(opts) [polishing - medaka (1 of 2)] tensorflow.python.framework.errors_impl.InternalError: cudaGetDevice() failed. Status: CUDA driver version is insufficient for CUDA runtime version [polishing - medaka (1 of 2)] Failed to run medaka consensus. [dragonflye] Error running command: medaka_consensus -i READS.fq.gz -d flye/polish/racon/2/consensus.fasta -o flye/polish/medaka/1 -m r941_min_sup_g507 -t 12 2>&1 | sed 's/^/[polishing - medaka (1 of 2)] /' | tee -a dragonflye.log

Is it possible to force dragonflye to use medaka on cpus?

[rpetit3]

Full disclaimer, I have no GPU to test things on. But, I think you might need to update your cuda drivers on the system.

Otherwise, you can try adding --medaka_opts '--disable_cudnn'

[gaworj]

Added --medaka_opts '--disable_cudnn'

[dragonflye] Polishing with Medaka (2 rounds) [dragonflye] Running: medaka_consensus -i READS.fq.gz -d flye/polish/racon/2/consensus.fasta -o flye/polish/medaka/1 -m r941_min_sup_g507 -t 12 --disable_cudnn 2>&1 | sed 's/^/[polishing - medaka (1 of 2)] /' | tee -a dragonflye.log [polishing - medaka (1 of 2)] Invalid option: --. [dragonflye] Error running command: medaka_consensus -i READS.fq.gz -d flye/polish/racon/2/consensus.fasta -o flye/polish/medaka/1 -m r941_min_sup_g507 -t 12 --disable_cudnn 2>&1 | sed 's/^/[polishing - medaka (1 of 2)] /' | tee -a dragonflye.log

There is no option --disable_cudnn in medaka_consensus help.

[rpetit3]

Looking at this: https://datascience.stackexchange.com/questions/58845/how-to-disable-gpu-with-tensorflow

You might need to do this:

export CUDA_VISIBLE_DEVICES="-1"

OR 

export CUDA_VISIBLE_DEVICES=''

[gaworj]

After setting export CUDA_VISIBLE_DEVICES='' medaka finished successfully. Thanks a lot for your help!

Can you also add --prefix option in dragonflye to set the name of the final consensus file?

[rpetit3]

hi @gaworj

--prefix is available in v1.0.14. I'm going to go ahead and close this issue.

Cheers, Robert