redndgreen8 / hmcnc Goto Github PK
View Code? Open in Web Editor NEWHidden Markov Model based Copy number caller
hmcnc's Issues
Seg fault for viterbi
segmentation fault arising for viterbi on chr2 only(?!)
repeatmask failure for assembly
repeat mask in viter.to call only works for alignment hg38
install issue, scipy=0.15.0 not available
Hi,
I was pointed to this tool for PB HiFi data analysis
I built the env as instructed but when it comes to scipy=0.15.0 it is not found by conda (or mamba)
Any idea what I can do to fix this?
can I use the scipy version 1.7.3 proposed by mamba? (seems to work)
Also, is there a tutorial on how to use the commands? the dry command output is not very explicit on where to get the inputs!
Thanks
(hmcnc) :/opt/biotools/hmcnc/HMM$ conda list
# packages in environment at /opt/miniconda3/envs/hmcnc:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.0 mro_2
aioeasywebdav 2.4.0 py39hf3d152e_1001 conda-forge
aiohttp 3.8.1 py39h7f8727e_1
aiosignal 1.2.0 pyhd3eb1b0_0
amply 0.1.5 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyhd3eb1b0_0
async-timeout 4.0.1 pyhd3eb1b0_0
attmap 0.13.2 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd3eb1b0_0
bcrypt 3.2.0 py39he8ac12f_0
bedtools 2.30.0 h468198e_3 bioconda
binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
blas 1.0 openblas
boost 1.73.0 py39h06a4308_11
boto3 1.21.32 pyhd3eb1b0_0
botocore 1.24.32 pyhd3eb1b0_0
bottleneck 1.3.4 py39hce1f21e_0
brotlipy 0.7.0 py39h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.4.26 h06a4308_0
cachetools 4.2.2 pyhd3eb1b0_0
cairo 1.16.0 h19f5f5c_2
certifi 2022.5.18.1 py39h06a4308_0
cffi 1.15.0 py39hd667e15_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
coin-or-cbc 2.10.8 h3786ebc_0 conda-forge
coin-or-cgl 0.60.6 he2f9439_0 conda-forge
coin-or-clp 1.17.6 h59210d1_1 conda-forge
coin-or-osi 0.108.7 h3b589db_0 conda-forge
coin-or-utils 2.11.4 hd28eb2d_1 conda-forge
coincbc 2.10.8 0_metapackage conda-forge
configargparse 1.4 pyhd3eb1b0_0
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
cryptography 37.0.1 py39h9ce1e76_0
curl 7.82.0 h7f8727e_0
datrie 0.8.2 py39h27cfd23_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
docutils 0.18.1 py39h06a4308_2
dpath 2.0.6 py39hf3d152e_1 conda-forge
dropbox 11.14.0 py39h06a4308_0
filechunkio 1.8 py_2 conda-forge
filelock 3.6.0 pyhd3eb1b0_0
fontconfig 2.13.1 h6c09931_0
freetype 2.11.0 h70c0345_0
fribidi 1.0.10 h7b6447c_0
frozenlist 1.2.0 py39h7f8727e_0
ftputil 5.0.4 pyhd8ed1ab_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
gfortran_impl_linux-64 7.3.0 hdf63c60_1
gfortran_linux-64 7.3.0 h553295d_15
gitdb 4.0.7 pyhd3eb1b0_0
gitpython 3.1.18 pyhd3eb1b0_1
glib 2.69.1 h4ff587b_1
google-api-core 1.31.5 pyhd8ed1ab_0 conda-forge
google-api-python-client 2.49.0 pyhd8ed1ab_0 conda-forge
google-auth 1.33.0 pyhd3eb1b0_0
google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge
google-cloud-core 1.7.1 pyhd3eb1b0_0
google-cloud-storage 1.41.0 pyhd3eb1b0_0
google-crc32c 1.1.2 py39h27cfd23_0
google-resumable-media 1.3.1 pyhd3eb1b0_1
googleapis-common-protos 1.53.0 py39h06a4308_0
graphite2 1.3.14 h295c915_1
grpcio 1.42.0 py39hce63b2e_0
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
harfbuzz 2.8.1 h6f93f22_0
htslib 1.15.1 h9753748_0 bioconda
httplib2 0.20.4 pyhd8ed1ab_0 conda-forge
icu 58.2 he6710b0_3
idna 3.3 pyhd3eb1b0_0
importlib-metadata 4.11.3 py39h06a4308_0
iniconfig 1.1.1 pyhd3eb1b0_0
jinja2 3.0.3 pyhd3eb1b0_0
jmespath 0.10.0 pyhd3eb1b0_0
jsonschema 4.4.0 py39h06a4308_0
jupyter_core 4.10.0 py39h06a4308_0
krb5 1.19.2 hac12032_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.9.0 13_linux64_openblas conda-forge
libboost 1.73.0 h3ff78a5_11
libcblas 3.9.0 13_linux64_openblas conda-forge
libcrc32c 1.1.1 he6710b0_2
libcurl 7.82.0 h0b77cf5_0
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libffi 3.3 he6710b0_2
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 12.1.0 h8d9b700_16 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
liblapacke 3.9.0 13_linux64_openblas conda-forge
libnghttp2 1.46.0 hce63b2e_0
libopenblas 0.3.18 hf726d26_0
libpng 1.6.37 hbc83047_0
libprotobuf 3.20.1 h4ff587b_0
libsodium 1.0.18 h7b6447c_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libuuid 1.0.3 h7f8727e_2
libxcb 1.15 h7f8727e_0
libxml2 2.9.14 h74e7548_0
libzlib 1.2.12 h166bdaf_0 conda-forge
logmuse 0.2.6 pyh8c360ce_0 conda-forge
lz4-c 1.9.3 h295c915_1
make 4.2.1 h1bed415_1
markupsafe 2.0.1 py39h27cfd23_0
mro-base 3.5.1 3
mro-base_impl 3.5.1 h9a62091_0
mro-basics 3.5.1 0
multidict 5.2.0 py39h7f8727e_2
nbformat 5.3.0 py39h06a4308_0
ncurses 6.3 h7f8727e_2
numexpr 2.8.1 py39hecfb737_0
numpy 1.22.3 py39h7a5d4dd_0
numpy-base 1.22.3 py39hb8be1f0_0
oauth2client 4.1.3 py_0 conda-forge
openssl 1.1.1o h7f8727e_0
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.2 py39h295c915_0
pango 1.45.3 hd140c19_0
paramiko 2.8.1 pyhd3eb1b0_0
pcre 8.45 h295c915_0
peppy 0.31.2 pyhd8ed1ab_2 conda-forge
pip 21.2.4 py39h06a4308_0
pixman 0.40.0 h7f8727e_1
plac 1.3.4 pyhd3eb1b0_0
pluggy 1.0.0 py39h06a4308_1
ply 3.11 py39h06a4308_0
prettytable 3.3.0 pyhd8ed1ab_0 conda-forge
protobuf 3.20.1 py39h295c915_0
psutil 5.8.0 py39h27cfd23_1
pulp 2.6.0 py39hf3d152e_1 conda-forge
py 1.11.0 pyhd3eb1b0_0
py-boost 1.73.0 py39ha9443f7_11
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycparser 2.21 pyhd3eb1b0_0
pygments 2.11.2 pyhd3eb1b0_0
pynacl 1.4.0 py39he8ac12f_1
pyopenssl 22.0.0 pyhd3eb1b0_0
pyparsing 3.0.4 pyhd3eb1b0_0
pyrsistent 0.18.0 py39heee7806_0
pysftp 0.2.9 pyhd3eb1b0_1
pysocks 1.7.1 py39h06a4308_0
pytest 7.1.1 py39h06a4308_0
python 3.9.12 h12debd9_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.15.1 pyhd3eb1b0_0
python-irodsclient 1.1.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.3 pyhd3eb1b0_0
pyyaml 6.0 py39h7f8727e_1
r 3.5.1 mro351_0
r-boot 1.3_20 mro351_0
r-checkpoint 0.4.4 mro351_0
r-class 7.3_14 mro351hd10c6a6_0
r-cluster 2.0.7_1 mro351hac1494b_0
r-codetools 0.2_15 mro351hf348343_0
r-curl 3.2 mro351hd10c6a6_1
r-deployrrserve 9.0.0 mro351_0
r-doparallel 1.0.13 mro351_0
r-foreach 1.5.0 mro351_0
r-foreign 0.8_70 mro351_0
r-iterators 1.0.10 mro351hf348343_0
r-jsonlite 1.5 mro351hd10c6a6_0
r-kernsmooth 2.23_15 mro351hac1494b_0
r-lattice 0.20_35 mro351hd10c6a6_0
r-mass 7.3_49 mro351_0
r-matrix 1.2_14 mro351hac1494b_0
r-mgcv 1.8_23 mro351_0
r-microsoftr 3.5.0.108 mro351_0
r-nlme 3.1_137 mro351hac1494b_0
r-nnet 7.3_12 mro351hd10c6a6_0
r-png 0.1_7 mro351hd10c6a6_0
r-r6 2.2.2 mro351hf348343_0
r-recommended 3.5.1 mro351_0
r-revoioq 10.0.0 mro351_0
r-revomods 11.0.0 mro351_0
r-revoutils 11.0.0 mro351_0
r-revoutilsmath 11.0.0 mro351_0
r-rpart 4.1_13 mro351hd10c6a6_0
r-runit 0.4.26 mro351_0
r-spatial 7.3_11 mro351_0
r-survival 2.41_3 mro351_0
ratelimiter 1.2.0 py_1002 conda-forge
readline 8.1.2 h7f8727e_1
requests 2.27.1 pyhd3eb1b0_0
retry 0.9.2 py_0 conda-forge
rsa 4.7.2 pyhd3eb1b0_1
s3transfer 0.5.0 pyhd3eb1b0_0
samtools 1.15.1 h1170115_0 bioconda
setuptools 61.2.0 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
slacker 0.14.0 py_0 conda-forge
smart_open 5.2.1 py39h06a4308_0
smmap 4.0.0 pyhd3eb1b0_0
snakemake 7.8.1 hdfd78af_0 bioconda
snakemake-minimal 7.8.1 pyhdfd78af_0 bioconda
sqlite 3.38.3 hc218d9a_0
stone 3.2.1 pyhd3eb1b0_0
stopit 1.1.2 py_0 conda-forge
tabix 1.11 hdfd78af_0 bioconda
tabulate 0.8.9 py39h06a4308_0
tk 8.6.11 h1ccaba5_1
tomli 1.2.2 pyhd3eb1b0_0
toposort 1.7 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd3eb1b0_0
typing-extensions 4.1.1 hd3eb1b0_0
typing_extensions 4.1.1 pyh06a4308_0
tzdata 2022a hda174b7_0
ubiquerg 0.6.1 pyh9f0ad1d_0 conda-forge
uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge
urllib3 1.26.9 py39h06a4308_0
veracitools 0.1.3 py_0 conda-forge
wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.37.1 pyhd3eb1b0_0
wrapt 1.13.3 py39h7f8727e_2
xz 5.2.5 h7f8727e_1
yaml 0.2.5 h7b6447c_0
yarl 1.5.1 py39h07f9747_0 conda-forge
yte 1.4.0 py39hf3d152e_0 conda-forge
zipp 3.8.0 py39h06a4308_0
zlib 1.2.12 h166bdaf_0 conda-forge
zstd 1.4.9 haebb681_0
asm.smk update
need to update and test assembly hmm
tabix integration
ref hg38 abstraction
masking with centromere,gap,telomere etc.. needs to be handled if not running human genome
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