Unicycler issue

[xlinxlin]

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 (Pilon step runs out of error (java.lang.OutOfMemoryError) rrwick/Unicycler#147).
2. Unicycler 0.4.8 maybe also works but it has conflicts with MultiQC in the conda environment.