BOL

For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail.

Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/home/RASflow
If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

samtools index mappedPairs.sorted.bam return the following error ...

[bam_sort_core] merging from 0 files and 2 in-memory blocks...
[E::hts_idx_push] Chromosome blocks not continuous
samtools index: failed to create index for "mappedPairs.sorted.bam"

While working with illumina data, I came cross chastity filter.  I am wondering about it !

(base) lege@Bathymodiolus:~$ ./alienomics_v0.3.1
Can't load '/tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273cf03dd05ad45721b/5b8c5ac2.so' for module POSIX: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273cf03dd05ad45721b/5b8c5ac2.so) at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187.
at /usr/local/share/perl/5.26.1/PAR/Heavy.pm line 140.
Compilation failed in require at script/alienomics_v0.3.pl line 28.
BEGIN failed--compilation aborted at script/alienomics_v0.3.pl line 28.

[main] Real time: 2.026 sec; CPU: 1.798 sec
Plotting the coverage
Error in library(reshape) : there is no package called ‘reshape’
Execution halted
./setu.sh -k yes -m pe -t 1 -r SRR11140750_1.fastq.gz,SRR11140750_2.fastq.gz 11,91s user 1,30s system 125% cpu 10,533 total

How to find the location of the module installed

$ conda install -c jnarayan81 alienomics

The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

- defaults/linux-64::jupyter==1.0.0=py37_7
  - defaults/noarch::pygments==2.5.2=py_0
  - defaults/noarch::jupyter_console==6.1.0=py_0
  - defaults/linux-64::spyder==4.0.1=py37_0
  - defaults/linux-64::bleach==3.1.0=py37_0
  - defaults/noarch::pytest-astropy==0.8.0=py_0
  - defaults/linux-64::scikit-learn==0.22.1=py37hd81dba3_0
  - defaults/linux-64::conda-build==3.18.11=py37_0
  - defaults/linux-64::nbconvert==5.6.1=py37_0
  - defaults/noarch::jupyterlab_server==1.0.6=py_0
  - defaults/noarch::qtconsole==4.6.0=py_1
  - defaults/noarch::flask==1.1.1=py_0
  - defaults/linux-64::anaconda==2020.02=py37_0
  - defaults/noarch::autopep8==1.4.4=py_0
  - defaults/linux-64::ipykernel==5.1.4=py37h39e3cac_0
  - defaults/linux-64::jsonschema==3.2.0=py37_0
  - defaults/linux-64::pytest-arraydiff==0.3=py37h39e3cac_0
  - defaults/linux-64::sympy==1.5.1=py37_0
  - defaults/linux-64::anaconda-client==1.7.2=py37_0
  - defaults/linux-64::pylint==2.4.4=py37_0
  - defaults/noarch::conda-verify==3.4.2=py_1
  - defaults/noarch::numpydoc==0.9.2=py_0
  - defaults/linux-64::ipython==7.12.0=py37h5ca1d4c_0
  - defaults/linux-64::astropy==4.0=py37h7b6447c_0
  - defaults/linux-64::spyder-kernels==1.8.1=py37_0
  - defaults/noarch::backports.functools_lru_cache==1.6.1=py_0
  - defaults/linux-64::clyent==1.2.2=py37_1
  - defaults/linux-64::pytest-remotedata==0.3.2=py37_0
  - defaults/noarch::jinja2==2.11.1=py_0
  - defaults/noarch::ipywidgets==7.5.1=py_0
  - defaults/linux-64::python-language-server==0.31.7=py37_0
  - defaults/noarch::jupyterlab==1.2.6=pyhf63ae98_0
  - defaults/linux-64::_ipyw_jlab_nb_ext_conf==0.1.0=py37_0
  - defaults/linux-64::matplotlib==3.1.3=py37_0
  - defaults/noarch::networkx==2.4=py_0
  - defaults/linux-64::flake8==3.7.9=py37_0
  - defaults/noarch::prompt_toolkit==3.0.3=py_0
  - defaults/linux-64::anaconda-navigator==1.9.12=py37_0
  - defaults/noarch::nbformat==5.0.4=py_0
  - defaults/noarch::pytest-astropy-header==0.1.2=py_0
  - defaults/noarch::joblib==0.14.1=py_0
  - defaults/noarch::seaborn==0.10.0=py_0
  - defaults/linux-64::distributed==2.11.0=py37_0
  - defaults/noarch::pytest-openfiles==0.4.0=py_0
  - defaults/linux-64::isort==4.3.21=py37_0
  - defaults/linux-64::wheel==0.34.2=py37_0
  - defaults/linux-64::bokeh==1.4.0=py37_0
  - defaults/linux-64::numba==0.48.0=py37h0573a6f_0
  - defaults/linux-64::conda==4.9.0=py37_0
  - defaults/noarch::dask==2.11.0=py_0
  - defaults/linux-64::nose==1.3.7=py37_2
  - defaults/noarch::anaconda-project==0.8.4=py_0
  - defaults/linux-64::notebook==6.0.3=py37_0
  - defaults/linux-64::widgetsnbextension==3.5.1=py37_0
  - defaults/linux-64::matplotlib-base==3.1.3=py37hef1b27d_0
  - defaults/noarch::pytest-doctestplus==0.5.0=py_0
  - defaults/linux-64::astroid==2.3.3=py37_0
  - defaults/linux-64::scikit-image==0.16.2=py37h0573a6f_0