problem in
sinamajidian opened this issue · 6 comments
Hi
I need a program for calling variants on Pacbio reads. Freebayes is very slow (10 hours for 1Mbp reference genome) and most of the variants are missed with the coverage of 50. I hope that your package can help me.
I installed using these line (I have not curl)
git clone --depth=1 https://github.com/aquaskyline/Clairvoyante.git
cd Clairvoyante
wget http://www.bio8.cs.hku.hk/trainedModels.tbz
tar trainedModels.tbz -jxf
pip install tensorflow --user
pip install blosc --user
pip install intervaltree --user
pip install numpy --user
wget 'http://www.bio8.cs.hku.hk/training.tar'
tar -xf training.tar
Firstly, "Quick Start with Variant Calling" is a bit unclear for me. when I download from "I need some results now" part, what should I do then to get some demo variant calls?
Next part titled "Call variants from at known variant sites using a BAM file and a trained model" needs testingData folder which i did not download it. So, I dismiss it and run the next part.
I run
python ../clairvoyante/callVar.py --chkpnt_fn ../trainedModels/fullv3-illumina-novoalign-hg001+hg002-hg38/learningRate1e-3.epoch500 --tensor_fn tensor_can_chr21 --call_fn tensor_can_chr21.vcf
and faced this:
Loading model ...
From /mnt/scratch/majid001/installed/Clairvoyante/clairvoyante/clairvoyante_v3.py:60: conv2d (from tensorflow.python.layers.convolutional) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.conv2d instead.
From /home/majid001/.local/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
From /mnt/scratch/majid001/installed/Clairvoyante/clairvoyante/clairvoyante_v3.py:66: max_pooling2d (from tensorflow.python.layers.pooling) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.max_pooling2d instead.
From /mnt/scratch/majid001/installed/Clairvoyante/clairvoyante/clairvoyante_v3.py:108: dense (from tensorflow.python.layers.core) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.dense instead.
From /home/majid001/.local/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
Restoring parameters from /mnt/scratch/majid001/installed/Clairvoyante/trainedModels/fullv3-illumina-novoalign-hg001+hg002-hg38/learningRate1e-3.epoch500
Traceback (most recent call last):
File "../clairvoyante/callVar.py", line 266, in <module>
main()
File "../clairvoyante/callVar.py", line 262, in main
Run(args)
File "../clairvoyante/callVar.py", line 47, in Run
Test(args, m, utils)
File "../clairvoyante/callVar.py", line 183, in Test
PrintVCFHeader(args, call_fh)
File "../clairvoyante/callVar.py", line 157, in PrintVCFHeader
print >> call_fh, '##fileformat=VCFv4.1'
TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. Did you mean "print(<message>, file=<output_stream>)"?
Versions and files in folder
python -c 'import tensorflow as tf; print(tf.__version__)'
1.13.1
python --version
Python 3.6.7
/mnt/scratch/majid001/installed/Clairvoyante$ ls
LICENSE.md clairvoyante dataPrepScripts port23.py python_requirements.txt training
README.md clairvoyante.py jupyter_nb pypy_requirements.txt trainedModels
Would you please help me?
Please use python 2.7.
Sorry for asking basic questions. I should read instruction carefully. I'm thankful for your quick reply. That's working now.
Then, I put my reference genome and aligned reads to the folder mydata
, and run this
python2 clairvoyante/callVarBamParallel.py \
--chkpnt_fn trainedModels/fullv3-pacbio-ngmlr-hg001-hg19/learningRate1e-3.epoch999 \
--ref_fn mydata/ref.fasta \
--bam_fn mydata/reads.bam \
--sampleName a \
--output_prefix b \
--threshold 0.125 \
--minCoverage 4 \
--tensorflowThreads 4 \
> commands.sh
and faced this Error: pypy executable not found
.
I should install pypy beforehand.
How about callVarBam.py
? It seems that it also needs pypy.
Is there any version which works without pypy?
Please install pypy following the README. It doesn't require admin privilege and is not hard.