nf-core/denovohybrid

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

denovohybrid's Issues

Unicycler issue

Hi!

The issue in Unicycler 0.4.7 (rrwick/Unicycler#140) has not been resolved, I have downgraded it to 0.4.4 to make it work.
Here is the output of the command conda env export

name: denovohybrid
channels:
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _r-mutex=1.0.0=anacondar_1
  - bandage=0.8.1=hb59a952_0
  - bcftools=1.7=0
  - binutils_impl_linux-64=2.33.1=he6710b0_7
  - binutils_linux-64=2.33.1=h9595d00_15
  - biopython=1.68=py35_0
  - blas=1.0=mkl
  - blast=2.5.0=hc0b0e79_3
  - boost=1.67.0=py35_4
  - bowtie2=2.3.4.3=py35h2d50403_0
  - bwidget=1.9.11=1
  - bzip2=1.0.8=h7b6447c_0
  - ca-certificates=2020.6.24=0
  - cairo=1.14.12=h8948797_3
  - certifi=2018.8.24=py35_1
  - circos=0.69.8=0
  - click=7.1.2=py_0
  - curl=7.55.1=h78862de_4
  - cycler=0.10.0=py35hc4d5149_0
  - dbus=1.13.16=hb2f20db_0
  - entrez-direct=13.3=pl526h375a9b1_0
  - expat=2.2.9=he6710b0_2
  - fastqc=0.11.9=0
  - filtlong=0.2.0=he941832_2
  - font-ttf-dejavu-sans-mono=2.37=h6964260_0
  - fontconfig=2.13.0=h9420a91_0
  - freebayes=1.2.0=py35h82df9c4_3
  - freetype=2.10.2=h5ab3b9f_0
  - fribidi=1.0.9=h7b6447c_0
  - 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
  - giflib=5.1.4=h14c3975_1
  - git=2.18.0=pl526hb37396a_0
  - glib=2.63.1=h5a9c865_0
  - glimmerhmm=3.0.4=pl526hf484d3e_3
  - graphite2=1.3.14=h23475e2_0
  - gsl=2.4=h14c3975_4
  - gst-plugins-base=1.14.0=hbbd80ab_1
  - gstreamer=1.14.0=hb453b48_1
  - gxx_impl_linux-64=7.3.0=hdf63c60_1
  - gxx_linux-64=7.3.0=h553295d_15
  - harfbuzz=1.8.8=hffaf4a1_0
  - htslib=1.7=0
  - icu=58.2=he6710b0_3
  - intel-openmp=2019.4=243
  - jinja2=2.11.2=py_0
  - joblib=0.14.1=py_0
  - jpeg=9b=h024ee3a_2
  - k8=0.2.5=he513fc3_0
  - kiwisolver=1.0.1=py35hf484d3e_0
  - krb5=1.16.1=hc83ff2d_6
  - ld_impl_linux-64=2.33.1=h53a641e_7
  - libboost=1.67.0=h46d08c1_4
  - libcurl=7.61.1=heec0ca6_0
  - libdeflate=1.0=h14c3975_1
  - libedit=3.1.20181209=hc058e9b_0
  - libffi=3.2.1=hd88cf55_4
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=9.1.0=hdf63c60_0
  - libgd=2.2.5=h0db58fd_3
  - libgfortran-ng=7.3.0=hdf63c60_0
  - libpng=1.6.37=hbc83047_0
  - libssh2=1.8.0=h9cfc8f7_4
  - libstdcxx-ng=9.1.0=hdf63c60_0
  - libtiff=4.1.0=h2733197_1
  - libuuid=1.0.3=h1bed415_2
  - libwebp=1.0.1=h8e7db2f_0
  - libxcb=1.14=h7b6447c_0
  - libxml2=2.9.10=he19cac6_1
  - lz4-c=1.9.2=he6710b0_0
  - make=4.2.1=h1bed415_1
  - markupsafe=1.0=py35h14c3975_1
  - matplotlib=3.0.0=py35h5429711_0
  - miniasm=0.3_r179=ha92aebf_0
  - minimap2=2.17=hed695b0_2
  - mkl=2018.0.3=1
  - mkl-service=1.1.2=py35h90e4bf4_5
  - mkl_fft=1.0.6=py35h7dd41cf_0
  - mkl_random=1.0.1=py35h4414c95_1
  - mmtf-python=1.0.2=py35_0
  - msgpack-python=0.5.6=py35h6bb024c_1
  - nanoget=1.13.2=py_0
  - nanomath=0.23.3=py_0
  - nanoplot=1.30.1=py_0
  - ncurses=6.1=he6710b0_1
  - ngs-bits=2018_04=py35_0
  - numpy=1.15.2=py35h1d66e8a_0
  - numpy-base=1.15.2=py35h81de0dd_0
  - olefile=0.46=py_0
  - openjdk=8.0.152=h7b6447c_3
  - openssl=1.0.2u=h7b6447c_0
  - pandas=0.23.4=py35h04863e7_0
  - pango=1.42.4=h049681c_0
  - parallel=20160622=1
  - patsy=0.5.0=py35_0
  - pauvre=0.1.86=py_1
  - pcre=8.44=he6710b0_0
  - perl=5.26.2=h14c3975_0
  - perl-app-cpanminus=1.7044=pl526_1
  - perl-archive-tar=2.32=pl526_0
  - perl-autoloader=5.74=pl526_2
  - perl-base=2.23=pl526_1
  - perl-business-isbn=3.004=pl526_0
  - perl-business-isbn-data=20140910.003=pl526_0
  - perl-carp=1.38=pl526_3
  - perl-clone=0.42=pl526h516909a_0
  - perl-common-sense=3.74=pl526_2
  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
  - perl-config-general=2.63=pl526_0
  - perl-constant=1.33=pl526_1
  - perl-data-dumper=2.173=pl526_0
  - perl-digest-hmac=1.03=pl526_3
  - perl-digest-md5=2.55=pl526_0
  - perl-digest-perl-md5=1.9=pl526_1
  - perl-dynaloader=1.25=pl526_1
  - perl-encode=2.88=pl526_1
  - perl-encode-locale=1.05=pl526_6
  - perl-exporter=5.72=pl526_1
  - perl-exporter-tiny=1.002001=pl526_0
  - perl-extutils-makemaker=7.36=pl526_1
  - perl-file-listing=6.04=pl526_1
  - perl-file-path=2.16=pl526_0
  - perl-file-temp=0.2304=pl526_2
  - perl-font-ttf=1.06=pl526_0
  - perl-gd=2.71=pl526he860b03_0
  - perl-html-parser=3.72=pl526h6bb024c_5
  - perl-html-tagset=3.20=pl526_3
  - perl-html-tree=5.07=pl526_1
  - perl-http-cookies=6.04=pl526_0
  - perl-http-daemon=6.01=pl526_1
  - perl-http-date=6.02=pl526_3
  - perl-http-message=6.18=pl526_0
  - perl-http-negotiate=6.01=pl526_3
  - perl-io-compress=2.087=pl526he1b5a44_0
  - perl-io-html=1.001=pl526_2
  - perl-io-socket-ssl=2.066=pl526_0
  - perl-io-string=1.08=pl526_3
  - perl-io-zlib=1.10=pl526_2
  - perl-json=4.02=pl526_0
  - perl-json-xs=2.34=pl526h6bb024c_3
  - perl-libwww-perl=6.39=pl526_0
  - perl-list-moreutils=0.428=pl526_1
  - perl-list-moreutils-xs=0.428=pl526_0
  - perl-lwp-mediatypes=6.04=pl526_0
  - perl-lwp-protocol-https=6.07=pl526_4
  - perl-math-bezier=0.01=pl526_1
  - perl-math-round=0.07=pl526_1
  - perl-math-vecstat=0.08=pl526_1
  - perl-mime-base64=3.15=pl526_1
  - perl-module-implementation=0.09=pl526_2
  - perl-module-runtime=0.016=pl526_1
  - perl-mozilla-ca=20180117=pl526_1
  - perl-net-http=6.19=pl526_0
  - perl-net-ssleay=1.85=pl526h9dad42d_0
  - perl-ntlm=1.09=pl526_4
  - perl-number-format=1.75=pl526_3
  - perl-params-validate=1.29=pl526h14c3975_1
  - perl-parent=0.236=pl526_1
  - perl-pathtools=3.75=pl526h14c3975_1
  - perl-readonly=2.05=pl526_0
  - perl-regexp-common=2017060201=pl526_0
  - perl-scalar-list-utils=1.52=pl526h516909a_0
  - perl-set-intspan=1.19=pl526_1
  - perl-socket=2.027=pl526_1
  - perl-statistics-basic=1.6611=pl526_2
  - perl-storable=3.15=pl526h14c3975_0
  - perl-svg=2.84=pl526_0
  - perl-test-requiresinternet=0.05=pl526_0
  - perl-text-format=0.59=pl526_2
  - perl-threaded=5.26.0=0
  - perl-time-hires=1.9760=pl526h14c3975_1
  - perl-time-local=1.28=pl526_1
  - perl-try-tiny=0.30=pl526_1
  - perl-types-serialiser=1.0=pl526_2
  - perl-uri=1.76=pl526_0
  - perl-www-robotrules=6.02=pl526_3
  - perl-xml-namespacesupport=1.12=pl526_0
  - perl-xml-parser=2.44=pl526h4e0c4b3_7
  - perl-xml-sax=1.02=pl526_0
  - perl-xml-sax-base=1.09=pl526_0
  - perl-xml-sax-expat=0.51=pl526_3
  - perl-xml-simple=2.25=pl526_1
  - perl-xsloader=0.24=pl526_0
  - pillow=5.2.0=py35heded4f4_0
  - pilon=1.23=2
  - pip=10.0.1=py35_0
  - pixman=0.40.0=h7b6447c_0
  - plotly=4.8.2=py_0
  - porechop=0.2.3_seqan2.1.1=py35h2d50403_3
  - py-boost=1.67.0=py35h04863e7_4
  - pyparsing=2.4.7=py_0
  - pyqt=5.9.2=py35h05f1152_2
  - pysam=0.14.1=py35_htslib1.7_0
  - python=3.5.6=hc3d631a_0
  - python-dateutil=2.8.1=py_0
  - pytz=2020.1=py_0
  - pyyaml=3.12=py35h46ef4ae_1
  - qt=5.9.6=h8703b6f_2
  - quast=5.0.2=py35pl526ha92aebf_0
  - r-base=3.5.1=h1e0a451_2
  - r-markdown=0.8=r351h96ca727_0
  - r-mime=0.5=r351h96ca727_0
  - racon=1.4.13=he513fc3_0
  - readline=7.0=h7b6447c_5
  - reportlab=3.4.0=py35_0
  - retrying=1.3.3=py_2
  - samtools=1.7=1
  - scipy=1.1.0=py35hfa4b5c9_1
  - seaborn=0.9.0=pyh91ea838_1
  - seqtk=1.3=hed695b0_2
  - setuptools=40.2.0=py35_0
  - simplejson=3.8.1=py35_0
  - sip=4.19.8=py35hf484d3e_0
  - six=1.15.0=py_0
  - spades=3.13.1=0
  - sqlite=3.31.1=h7b6447c_0
  - statsmodels=0.9.0=py35h3010b51_0
  - tbb=2020.0=hfd86e86_0
  - tbb4py=2018.0.5=py35h6bb024c_0
  - tk=8.6.10=hbc83047_0
  - tktable=2.10=h14c3975_0
  - tornado=5.1.1=py35h7b6447c_0
  - unicycler=0.4.4=py35_0
  - wheel=0.31.1=py35_0
  - wtdbg=2.5=h8b12597_0
  - xz=5.2.5=h7b6447c_0
  - yaml=0.2.5=h7b6447c_0
  - zlib=1.2.11=h7b6447c_3
  - zstd=1.4.4=h0b5b093_3
  - pip:
    - multiqc==0.9
prefix: /home/sysgen/miniconda3/envs/denovohybrid

By the last process multiqc there was an error and the run stopped:

multiqc : Oops! The 'custom_content' MultiQC module broke...

But the output can still be found in the nextflow work directory and it looks good.

Others:

1. The memory limit in Pilon need to be set to 8GB or above (rrwick/Unicycler#147).
2. Unicycler 0.4.8 maybe also works but it has conflicts with MultiQC in the conda environment.

Fix TEMPLATE branch

Hi there!

It looks this pipeline has a TEMPLATE branch (great!), however it has no shared history which means that the automated template synchronisation does not work.

In order to fix this for future pipeline syncs, you need to do one fully manual merge. The method for this is documented here: https://nf-co.re/developers/sync#merge-template-into-main-branches
The key is basically to supply --allow-unrelated-histories when running the merge.

You'll need to pull the template changes to your fork first, see these docs.

Once you've done this once, there will be shared history, and future automated sync PRs should work.. Let me know if you need any help.

Phil

x-ref nf-core/tools#548 (comment)

probable typo in doc

thanks for the pipeline, looking forward to try it as soon as I figure out local nextflow deployment on my server

wtdbg2
Wtdbg2 is a very recent, and extremely fast long read assembler. It can bei also used to assemble large genomes. A human genome takes about 30 CPU hours and 220Gb of memory. Similar to miniasm, wtdbg2 is also followed by a racon consensus step and a short read polishing using Pilon if available.

--mode miniasm **(should be '--mode wtdbg2' right?)**