BOL

I am working on a new genome, and wondering about prediction methods for heterozygosity in the genome. Any tools suggestions and helps are welcome. 

whatshap phase -o seeWhat.vcf --reference genome.fa see.vcf genome.fa.sorted.bam

This is WhatsHap 0.17 running under Python 3.6.6
Traceback (most recent call last):
File "/home/anaconda3/bin/whatshap", line 11, in <module>
load_entry_point('whatshap==0.17', 'console_scripts', 'whatshap')()
File "/home/anaconda3/lib/python3.6/site-packages/whatshap/__main__.py", line 83, in main
module.main(args)
File "/home/anaconda3/lib/python3.6/site-packages/whatshap/phase.py", line 1089, in main
run_whatshap(**vars(args))
File "/home/anaconda3/lib/python3.6/site-packages/whatshap/phase.py", line 580, in run_whatshap
out_file=output, tag=tag)
File "/home/anaconda3/lib/python3.6/site-packages/whatshap/vcf.py", line 478, in __init__
self._reader = vcf.Reader(filename=in_path)
File "/home/anaconda3/lib/python3.6/site-packages/vcf/parser.py", line 300, in __init__
self._parse_metainfo()
File "/home/anaconda3/lib/python3.6/site-packages/vcf/parser.py", line 317, in _parse_metainfo
line = next(self.reader)
File "/home/anaconda3/lib/python3.6/site-packages/vcf/parser.py", line 280, in <genexpr>
self.reader = (line.strip() for line in self._reader if line.strip())
File "/home/anaconda3/lib/python3.6/codecs.py", line 321, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

How to fix this error ? 

➜ OligoMiner git:(master) conda create --name probeMining numpy scipy biopython scikit-learn
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3/envs/probeMining

added / updated specs:
- biopython
- numpy
- scikit-learn
- scipy

The following packages will be downloaded:

package | build
---------------------------|-----------------
numpy-1.15.2 |py27_blas_openblashd3ea46f_1 4.2 MB conda-forge
python-2.7.15 | h33da82c_4 13.6 MB conda-forge
reportlab-3.5.9 | py27h77bcf2c_0 2.5 MB conda-forge
scikit-learn-0.20.0 |py27_blas_openblasha84fab4_201 13.5 MB conda-forge
biopython-1.68 | py27_0 2.5 MB bioconda
certifi-2018.10.15 | py27_1000 138 KB conda-forge
msgpack-python-0.5.6 | py27h2d50403_3 101 KB conda-forge
libpng-1.6.35 | ha92aebf_2 305 KB conda-forge
blas-1.1 | openblas 1 KB conda-forge
libtiff-4.0.9 | he6b73bb_2 521 KB conda-forge
openblas-0.2.20 | 8 17.0 MB conda-forge
mmtf-python-1.0.2 | py27_0 34 KB bioconda
scipy-1.1.0 |py27_blas_openblash7943236_201 39.4 MB conda-forge
olefile-0.46 | py_0 31 KB conda-forge
pillow-5.3.0 | py27hc736899_0 603 KB conda-forge
------------------------------------------------------------
Total: 94.3 MB

The following NEW packages will be INSTALLED:

biopython: 1.68-py27_0 bioconda
blas: 1.1-openblas conda-forge
ca-certificates: 2018.10.15-ha4d7672_0 conda-forge
certifi: 2018.10.15-py27_1000 conda-forge
freetype: 2.9.1-h6debe1e_4 conda-forge
jpeg: 9c-h470a237_1 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc-ng: 7.2.0-hdf63c60_3 conda-forge
libgfortran: 3.0.0-1 conda-forge
libpng: 1.6.35-ha92aebf_2 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
libtiff: 4.0.9-he6b73bb_2 conda-forge
mmtf-python: 1.0.2-py27_0 bioconda
msgpack-python: 0.5.6-py27h2d50403_3 conda-forge
ncurses: 6.1-hfc679d8_1 conda-forge
numpy: 1.15.2-py27_blas_openblashd3ea46f_1 conda-forge [blas_openblas]
olefile: 0.46-py_0 conda-forge
openblas: 0.2.20-8 conda-forge
openssl: 1.0.2p-h470a237_1 conda-forge
pillow: 5.3.0-py27hc736899_0 conda-forge
pip: 18.1-py27_1000 conda-forge
python: 2.7.15-h33da82c_4 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
reportlab: 3.5.9-py27h77bcf2c_0 conda-forge
scikit-learn: 0.20.0-py27_blas_openblasha84fab4_201 conda-forge [blas_openblas]
scipy: 1.1.0-py27_blas_openblash7943236_201 conda-forge [blas_openblas]
setuptools: 40.4.3-py27_0 conda-forge
sqlite: 3.25.2-hb1c47c0_0 conda-forge
tk: 8.6.8-ha92aebf_0 conda-forge
wheel: 0.32.1-py27_0 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
numpy-1.15.2 | 4.2 MB | ##################################### | 100%
python-2.7.15 | 13.6 MB | ##################################### | 100%
reportlab-3.5.9 | 2.5 MB | ##################################### | 100%
scikit-learn-0.20.0 | 13.5 MB | ##################################### | 100%
biopython-1.68 | 2.5 MB | ##################################### | 100%
certifi-2018.10.15 | 138 KB | ##################################### | 100%
msgpack-python-0.5.6 | 101 KB | ##################################### | 100%
libpng-1.6.35 | 305 KB | ##################################### | 100%
blas-1.1 | 1 KB | ##################################### | 100%
libtiff-4.0.9 | 521 KB | ##################################### | 100%
openblas-0.2.20 | 17.0 MB | ##################################### | 100%
mmtf-python-1.0.2 | 34 KB | ##################################### | 100%
scipy-1.1.0 | 39.4 MB | ##################################### | 100%
olefile-0.46 | 31 KB | ##################################### | 100%
pillow-5.3.0 | 603 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate probeMining
#
# To deactivate an active environment, use
#
# $ conda deactivate

➜ OligoMiner git:(master) conda activate probeMining

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with

$ echo ". /home/urbe/anaconda3/etc/profile.d/conda.sh" >> ~/.bashrc

or, for all users, enable conda with

$ sudo ln -s /home/urbe/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh

The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH. To do so, run

$ conda activate

in your terminal, or to put the base environment on PATH permanently, run

$ echo "conda activate" >> ~/.bashrc

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bashrc file. You should manually remove the line that looks like

export PATH="/home/urbe/anaconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bashrc file! ^^^

I receive this error while mapping with BWA MEM ! How to fix it ?

3C: chromosome conformation capture

4C:chromosome conformation capture-on-chip

5C : chromosome conformation capture carbon copy

While mapping minimap2 return following warning:

[WARNING] For a multi-part index, no @SQ lines will be outputted.

How to resolve it. 

I am working on a metazoan genome. I wanted to try the best known method to validate the assembly structure. Your suggestions are welcome. 

While installing Perl GD module, I got following error 

libgd not found !

I am unable to index fasta file with samtools ! It return "different line length in sequence" error message . How to fix it? 

nc@radha[Downloads] samtools faidx dedup.genome.scf.fasta_assembly.fna []
[fai_build_core] different line length in sequence 'jcf7180000001219'.
Could not build fai index dedup.genome.scf.fasta_assembly.fna.fai
nc@radha[Downloads] more dedup.genome.scf.fasta_assembly.fna| grep ">" | wc -l
336