Singularity default in make_anno.nf config

[luckysardar]

Thank for the newflow pipeline

I am running

docker build .

getting bellow error

Step 1/52 : FROM biocorecrg/centos-perlbrew-pyenv3-java:centos7
 ---> 669f4335d0ab
Step 2/52 : MAINTAINER Toni Hermoso Pulido <toni.hermoso@crg.eu>
 ---> Using cache
 ---> a614883ded8f
Step 3/52 : MAINTAINER Luca Cozzuto <lucacozzuto@gmail.com>
 ---> Using cache
 ---> f5ec43923789
Step 4/52 : ARG FASTQC_VERSION=0.11.9
 ---> Using cache
 ---> 890ae896d2f5
Step 5/52 : ARG STAR_VERSION=2.7.3a
 ---> Using cache
 ---> b6fa72b82912
Step 6/52 : ARG QUALIMAP_VERSION=2.2.1
 ---> Using cache
 ---> ef797180b8fb
Step 7/52 : ARG MULTIQC_VERSION=1.8
 ---> Using cache
 ---> b9b3b0ad0809
Step 8/52 : ARG SAMTOOLS_VERSION=1.10
 ---> Using cache
 ---> 086d4fdaf996
Step 9/52 : ARG TOOL_MULTIQC_VERSION=1.1
 ---> Using cache
 ---> 15e96d4b9131
Step 10/52 : ARG HTSEQ_VERSION=0.11.1
 ---> Using cache
 ---> ffb60001880e
Step 11/52 : ARG BEDTOOLS_VERSION=2.29.2
 ---> Using cache
 ---> 14c1d8aa72b3
Step 12/52 : ARG HTSLIB_VERSION=1.10.2
 ---> Using cache
 ---> 26740cc60139
Step 13/52 : RUN bash -c 'curl -k -L https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools.static.binary > /usr/local/bin/bedtools'
 ---> Using cache
 ---> fea7465f39d3
Step 14/52 : RUN chmod +x /usr/local/bin/bedtools
 ---> Using cache
 ---> 635a3d951d7c
Step 15/52 : RUN bash -c 'curl -k -L https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${FASTQC_VERSION}.zip > fastqc.zip'
 ---> Using cache
 ---> 3da1252b8106
Step 16/52 : RUN unzip fastqc.zip; chmod 775 FastQC/fastqc; ln -s $PWD/FastQC/fastqc /usr/local/bin/fastqc
 ---> Using cache
 ---> 15d1984e09cb
Step 17/52 : RUN bash -c 'curl -k -L https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz > STAR.tar.gz'
 ---> Using cache
 ---> d1a2c53a1d9d
Step 18/52 : RUN tar -zvxf STAR.tar.gz
 ---> Using cache
 ---> 92582278affa
Step 19/52 : RUN cp STAR-${STAR_VERSION}/bin/Linux_x86_64/* /usr/local/bin/
 ---> Using cache
 ---> d6092c409df2
Step 20/52 : RUN rm STAR.tar.gz
 ---> Using cache
 ---> 45b35689a2f0
Step 21/52 : RUN bash -c 'curl -k -L https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v${QUALIMAP_VERSION}.zip > qualimap.zip'
 ---> Using cache
 ---> a8ae3b0cb5f1
Step 22/52 : RUN unzip qualimap.zip
 ---> Using cache
 ---> e7129e401074
Step 23/52 : RUN rm qualimap.zip
 ---> Using cache
 ---> aff9a7243b63
Step 24/52 : RUN ln -s $PWD/qualimap_v${QUALIMAP_VERSION}/qualimap /usr/local/bin/
 ---> Using cache
 ---> 057398046625
Step 25/52 : RUN python3 -m pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git
 ---> Running in d5a1b04d39eb
Collecting git+https://github.com/ewels/MultiQC.git
  Cloning https://github.com/ewels/MultiQC.git to /tmp/pip-apb_2fnm-build
Collecting matplotlib>=2.1.1 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/09/03/b7b30fa81cb687d1178e085d0f01111ceaea3bf81f9330c937fb6f6c8ca0/matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5MB)
Collecting networkx>=2.5.1 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/f3/b7/c7f488101c0bb5e4178f3cde416004280fd40262433496830de8a8c21613/networkx-2.5.1-py3-none-any.whl (1.6MB)
Collecting numpy (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/45/b2/6c7545bb7a38754d63048c7696804a0d947328125d81bf12beaa692c3ae3/numpy-1.19.5-cp36-cp36m-manylinux1_x86_64.whl (13.4MB)
Collecting click (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/4a/a8/0b2ced25639fb20cc1c9784de90a8c25f9504a7f18cd8b5397bd61696d7d/click-8.0.4-py3-none-any.whl (97kB)
Collecting coloredlogs (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46kB)
Collecting future>0.14.0 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829kB)
Collecting jinja2>=3.0.0 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/20/9a/e5d9ec41927401e41aea8af6d16e78b5e612bca4699d417f646a9610a076/Jinja2-3.0.3-py3-none-any.whl (133kB)
Collecting lzstring (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/ab/0c/28347673b45e5f0975cdf1f6d69ede6ad049be873194c4e164d79aecd34c/lzstring-1.0.4.tar.gz
Collecting markdown (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/f3/df/ca72f352e15b6f8ce32b74af029f1189abffb906f7c137501ffe69c98a65/Markdown-3.3.7-py3-none-any.whl (97kB)
Collecting pyyaml>=4 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/b3/85/79b9e5b4e8d3c0ac657f4e8617713cca8408f6cdc65d2ee6554217cedff1/PyYAML-6.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (603kB)
Collecting requests (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/2d/61/08076519c80041bc0ffa1a8af0cbd3bf3e2b62af10435d269a9d0f40564d/requests-2.27.1-py2.py3-none-any.whl (63kB)
Collecting rich>=10 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/32/60/81ac2e7d1e3b861ab478a72e3b20fc91c4302acd2274822e493758941829/rich-12.6.0-py3-none-any.whl (237kB)
Collecting rich-click (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/2e/29/900393c3f7cc82104c6e93b3c57acbbd49d1a5da50a1c8fc52a3cc28543a/rich_click-1.2.1-py3-none-any.whl
Collecting simplejson (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/ec/e5/a4d5b615e4d3bf6ddde77b5f1c801adb869cb5ad565deda2402edc631388/simplejson-3.17.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (129kB)
Collecting spectra>=0.0.10 (from multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/50/50/ae8d87ab681a58e246215e51715566df8074a86d244fee31fa8585fe5f9f/spectra-0.0.11.tar.gz
Collecting python-dateutil>=2.1 (from matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 (from matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/80/c1/23fd82ad3121656b585351aba6c19761926bb0db2ebed9e4ff09a43a3fcc/pyparsing-3.0.7-py3-none-any.whl (98kB)
Collecting cycler>=0.10 (from matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/5c/f9/695d6bedebd747e5eb0fe8fad57b72fdf25411273a39791cde838d5a8f51/cycler-0.11.0-py3-none-any.whl
Collecting pillow>=6.2.0 (from matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/7d/2a/2fc11b54e2742db06297f7fa7f420a0e3069fdcf0e4b57dfec33f0b08622/Pillow-8.4.0.tar.gz (49.4MB)
Collecting kiwisolver>=1.0.1 (from matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/a7/1b/cbd8ae738719b5f41592a12057ef5442e2ed5f5cb5451f8fc7e9f8875a1a/kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1MB)
Collecting decorator<5,>=4.3 (from networkx>=2.5.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl
Collecting importlib-metadata; python_version < "3.8" (from click->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/a0/a1/b153a0a4caf7a7e3f15c2cd56c7702e2cf3d89b1b359d1f1c5e59d68f4ce/importlib_metadata-4.8.3-py3-none-any.whl
Collecting humanfriendly>=9.1 (from coloredlogs->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl (86kB)
Collecting MarkupSafe>=2.0 (from jinja2>=3.0.0->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/fc/d6/57f9a97e56447a1e340f8574836d3b636e2c14de304943836bd645fa9c7e/MarkupSafe-2.0.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting idna<4,>=2.5; python_version >= "3" (from requests->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/fc/34/3030de6f1370931b9dbb4dad48f6ab1015ab1d32447850b9fc94e60097be/idna-3.4-py3-none-any.whl (61kB)
Collecting urllib3<1.27,>=1.21.1 (from requests->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/6f/de/5be2e3eed8426f871b170663333a0f627fc2924cc386cd41be065e7ea870/urllib3-1.26.12-py2.py3-none-any.whl (140kB)
Collecting certifi>=2017.4.17 (from requests->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/1d/38/fa96a426e0c0e68aabc68e896584b83ad1eec779265a028e156ce509630e/certifi-2022.9.24-py3-none-any.whl (161kB)
Collecting charset-normalizer~=2.0.0; python_version >= "3" (from requests->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/06/b3/24afc8868eba069a7f03650ac750a778862dc34941a4bebeb58706715726/charset_normalizer-2.0.12-py3-none-any.whl
Collecting commonmark<0.10.0,>=0.9.0 (from rich>=10->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/b1/92/dfd892312d822f36c55366118b95d914e5f16de11044a27cf10a7d71bbbf/commonmark-0.9.1-py2.py3-none-any.whl (51kB)
Collecting pygments<3.0.0,>=2.6.0 (from rich>=10->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/4f/82/672cd382e5b39ab1cd422a672382f08a1fb3d08d9e0c0f3707f33a52063b/Pygments-2.13.0-py3-none-any.whl (1.1MB)
Collecting typing-extensions<5.0,>=4.0.0; python_version < "3.9" (from rich>=10->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/45/6b/44f7f8f1e110027cf88956b59f2fad776cca7e1704396d043f89effd3a0e/typing_extensions-4.1.1-py3-none-any.whl
Collecting dataclasses<0.9,>=0.7; python_version < "3.7" (from rich>=10->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/fe/ca/75fac5856ab5cfa51bbbcefa250182e50441074fdc3f803f6e76451fab43/dataclasses-0.8-py3-none-any.whl
Collecting colormath>=3.0.0 (from spectra>=0.0.10->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/ce/cf/70ea34103a76cc6fb1892289bda321cd0cc73b1a5500ee7fe9ef9f64acef/colormath-3.0.0.tar.gz
Collecting six>=1.5 (from python-dateutil>=2.1->matplotlib>=2.1.1->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl
Collecting zipp>=0.5 (from importlib-metadata; python_version < "3.8"->click->multiqc==1.14.dev0)
  Downloading https://files.pythonhosted.org/packages/bd/df/d4a4974a3e3957fd1c1fa3082366d7fff6e428ddb55f074bf64876f8e8ad/zipp-3.6.0-py3-none-any.whl
Installing collected packages: six, python-dateutil, pyparsing, numpy, cycler, pillow, kiwisolver, matplotlib, decorator, networkx, typing-extensions, zipp, importlib-metadata, click, humanfriendly, coloredlogs, future, MarkupSafe, jinja2, lzstring, markdown, pyyaml, idna, urllib3, certifi, charset-normalizer, requests, commonmark, pygments, dataclasses, rich, rich-click, simplejson, colormath, spectra, multiqc
  Running setup.py install for pillow: started
    Running setup.py install for pillow: finished with status 'error'
    Complete output from command /usr/local/python/versions/3.6.3/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-dir23ma_/pillow/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-v24jnr9g-record/install-record.txt --single-version-externally-managed --compile:
    /usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
      warnings.warn(msg)
    /usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'project_urls'
      warnings.warn(msg)
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/TiffImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/SunImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PpmImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/DcxImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageGrab.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ContainerIO.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageTransform.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/WmfImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageMath.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageMorph.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/IcoImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageFilter.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageFont.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/TiffTags.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/IcnsImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/XVThumbImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/BlpImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageQt.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/TarIO.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageMode.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GifImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/_binary.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/EpsImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageShow.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/BmpImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GimpGradientFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageChops.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GribStubImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/_util.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GdImageFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/FtexImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/MpegImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PcfFontFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/_version.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/WebPImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageOps.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/MpoImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/JpegPresets.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/FontFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageTk.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/WalImageFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PaletteFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PdfParser.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/FliImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/SgiImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageSequence.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/FpxImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/Hdf5StubImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/SpiderImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GimpPaletteFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/IptcImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/XbmImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageCms.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PngImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PsdImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageWin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/CurImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageStat.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/features.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/TgaImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/FitsStubImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImagePalette.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/_tkinter_finder.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PalmImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PdfImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageDraw2.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/Image.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/MspImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImtImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PcdImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/BdfFontFile.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/JpegImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PixarImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageDraw.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ExifTags.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/__main__.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/DdsImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PSDraw.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageEnhance.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PcxImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/XpmImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/Jpeg2KImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImageColor.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/GbrImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/McIdasImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/__init__.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/MicImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/BufrStubImagePlugin.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/PyAccess.py -> build/lib.linux-x86_64-3.6/PIL
    copying src/PIL/ImagePath.py -> build/lib.linux-x86_64-3.6/PIL
    running egg_info
    writing src/Pillow.egg-info/PKG-INFO
    writing dependency_links to src/Pillow.egg-info/dependency_links.txt
    writing top-level names to src/Pillow.egg-info/top_level.txt
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'src/Pillow.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching '*.c'
    warning: no files found matching '*.h'
    warning: no files found matching '*.sh'
    warning: no previously-included files found matching '.appveyor.yml'
    warning: no previously-included files found matching '.clang-format'
    warning: no previously-included files found matching '.coveragerc'
    warning: no previously-included files found matching '.editorconfig'
    warning: no previously-included files found matching '.readthedocs.yml'
    warning: no previously-included files found matching 'codecov.yml'
    warning: no previously-included files matching '.git*' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.so' found anywhere in distribution
    no previously-included directories found matching '.ci'
    writing manifest file 'src/Pillow.egg-info/SOURCES.txt'
    running build_ext

    The headers or library files could not be found for jpeg,
    a required dependency when compiling Pillow from source.

    Please see the install instructions at:
       https://pillow.readthedocs.io/en/latest/installation.html

    Traceback (most recent call last):
      File "/tmp/pip-build-dir23ma_/pillow/setup.py", line 1024, in <module>
        zip_safe=not (debug_build() or PLATFORM_MINGW),
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/setuptools/command/build_ext.py", line 75, in run
        _build_ext.run(self)
      File "/usr/local/python/versions/3.6.3/lib/python3.6/distutils/command/build_ext.py", line 339, in run
        self.build_extensions()
      File "/tmp/pip-build-dir23ma_/pillow/setup.py", line 790, in build_extensions
        raise RequiredDependencyException(f)
    __main__.RequiredDependencyException: jpeg

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-dir23ma_/pillow/setup.py", line 1037, in <module>
        raise RequiredDependencyException(msg)
    __main__.RequiredDependencyException:

    The headers or library files could not be found for jpeg,
    a required dependency when compiling Pillow from source.

    Please see the install instructions at:
       https://pillow.readthedocs.io/en/latest/installation.html

    ----------------------------------------
Command "/usr/local/python/versions/3.6.3/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-dir23ma_/pillow/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-v24jnr9g-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-dir23ma_/pillow/
You are using pip version 9.0.1, however version 22.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
The command '/bin/sh -c python3 -m pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git' returned a non-zero code: 1```

[lucacozzuto]

Hi, you don't need to rebuild the docker image for using the pipeline. The pipeline will download it for you from dockerhub. Sometimes rebuilding the images some dependencies are moved from repositories etc. So better to use the image we generated.

[luckysardar]

Thanks for the quick response,

I Have tried to run the pipeline

nextflow run make_anno.nf -with-docker -bg --vcffile mgp.v5.merged.snps_all.dbSNP142.vcf.gz --speciesA CAST_EiJ --speciesB 129S1_SvImJ --genome GRCm38_68.fa --outvcf CAST_EiJ-129S1_SvImJ.vcf > log

log file

N E X T F L O W ~ version 22.10.0 Launchingmake_anno.nf[mighty_ekeblad] DSL2 - revision: ea836071c0 Cannot enable more than one container engine -- Choose either one of: docker, singularity

[lucacozzuto]

Uh, you are right I set singularity as default. I changed it. Can you do a git pull and try again? Thanks for spotting the error.

[lucacozzuto]

Fixed at https://github.com/biocorecrg/allele_specific_RNAseq/commit/a468e368ab51d553900989a6dba97c843bb5b1ee

[luckysardar]

Okay Thanks i will do that and get back to you

[luckysardar]

Hello I have run the same command which was mentioned above gave me warning and no output was generated

log file

N E X T F L O W  ~  version 22.10.0
Launching `make_anno.nf` [tiny_raman] DSL2 - revision: ea836071c0

BIOCORE@CRG RNAseq - N F  ~  version 1.0

╔═╗┬  ┬  ┌─┐┬  ┌─┐  ╔═╗┌─┐┌─┐┌─┐┬┌─┐┬┌─┐  ╦═╗╔╗╔╔═╗┌─┐┌─┐┌─┐ 
╠═╣│  │  ├┤ │  ├┤   ╚═╗├─┘├┤ │  │├┤ ││    ╠╦╝║║║╠═╣└─┐├┤ │─┼┐
╩ ╩┴─┘┴─┘└─┘┴─┘└─┘  ╚═╝┴  └─┘└─┘┴└  ┴└─┘  ╩╚═╝╚╝╩ ╩└─┘└─┘└─┘└

====================================================
BIOCORE@CRG Allele Specific RNAseq - N F  ~  version 1.0
====================================================
vcffile                       : mgp.v5.merged.snps_all.dbSNP142.vcf.gz
speciesA                      : CAST_EiJ
speciesB                      : 129S1_SvImJ
genome                        : GRCm38_68.fa
outvcf                        : CAST_EiJ-129S1_SvImJ.vcf
email for notification        : mymail@mydomain.eu

warning

=============================================================================
=                                WARNING                                    =
= You are running this script using DSL2 syntax, however it does not        = 
= contain any 'workflow' definition so there's nothing for Nextflow to run. =
=                                                                           =
= If this script was written using Nextflow DSL1 syntax, please add the     = 
= setting 'nextflow.enable.dsl=1' to the nextflow.config file or use the    =
= command-line option '-dsl1' when running the pipeline.                    =
=                                                                           =
= More details at this link: https://www.nextflow.io/docs/latest/dsl2.html  =
=============================================================================

[lucacozzuto]

Yes, the newer version of nextflow assumes is DSL2. So... you have to add -dsl1 option when running nextflow. I'll add a note to the documentation

[luckysardar]

Thank you Its running now i will let you know if i face anything

[luckysardar]

hello again I got a error some permission error i have given all permission to nextflow and try to run as root user also but process did not completed

N E X T F L O W  ~  version 22.10.0
Launching `make_anno.nf` [evil_mandelbrot] DSL1 - revision: ea836071c0

BIOCORE@CRG RNAseq - N F  ~  version 1.0

╔═╗┬  ┬  ┌─┐┬  ┌─┐  ╔═╗┌─┐┌─┐┌─┐┬┌─┐┬┌─┐  ╦═╗╔╗╔╔═╗┌─┐┌─┐┌─┐ 
╠═╣│  │  ├┤ │  ├┤   ╚═╗├─┘├┤ │  │├┤ ││    ╠╦╝║║║╠═╣└─┐├┤ │─┼┐
╩ ╩┴─┘┴─┘└─┘┴─┘└─┘  ╚═╝┴  └─┘└─┘┴└  ┴└─┘  ╩╚═╝╚╝╩ ╩└─┘└─┘└─┘└

====================================================
BIOCORE@CRG Allele Specific RNAseq - N F  ~  version 1.0
====================================================
vcffile                       : mgp.v5.merged.snps_all.dbSNP142.vcf.gz
speciesA                      : CAST_EiJ
speciesB                      : 129S1_SvImJ
genome                        : GRCm38_68.fa
outvcf                        : CAST_EiJ-129S1_SvImJ.vcf
email for notification        : mymail@mydomain.eu

Error executing process > 'parseVCF (mgp.v5.merged.snps_all.dbSNP142.vcf.gz)'

Caused by:
  Unable to create directory=/Allelic_analysis_new/allele_specific_RNAseq/makeAnno/work/c8/93e60c21c12211cd17b010d93426c5 -- check file system permissions

Failed to invoke `workflow.onComplete` event handler

 -- Check script 'make_anno.nf' at line: 102 or see '.nextflow.log' file for more details
Pipeline BIOCORE@CRG Master of Pore completed!
Started at  2022-10-21T18:01:15.783383+05:30
Finished at 2022-10-21T18:01:16.614244+05:30
Time elapsed: 830ms
Execution status: failed

is it anything to do with system config I have 64GB ram with 12 core

[lucacozzuto]

this is weird. Can you please add -w $PWD/work to the command line? It looks like is trying to write to a place where you have no privileges... Are you using Linux or mac?

[luckysardar]

I am using linux

[lucacozzuto]

Let me know if you manage

[luckysardar]

Hello I have manage to ran as sudo user it ran succesfully, Got the output for the one of the sample SRR14004348 when I am checking allelic proportion chromsome wide data is biased towords one of the allele also same for other sample can you please suggest me anything i am missing. I just took mean across chromsomes. followed same pipeline with input file mentioned

what we expect from autosome should give almost 50:50 ratio most of the chromosome showing biased average ratio is it because of some aneuploidy or what please suggest

Thank you

chromosome   A/(A+B)       B/(A+B)
X   0.855416115526518   0.144583884473482
13  0.504994567271183   0.495005432728817
9   0.436021416100318   0.563978583899682
7   0.395250986658452   0.604749013341547
5   0.373462992941653   0.626537007058346
8   0.366074201526175   0.633925798473825
2   0.230499212359011   0.76950078764099
11  0.204298039835776   0.795701960164223
6   0.11859084240173    0.88140915759827
4   0.037873537098041   0.962126462901958
3   0.030748955771279   0.96925104422872
16  0.026845202408981   0.973154797591019
18  0.023344626780433   0.976655373219567
14  0.022645613522724   0.977354386477276
17  0.021418953610684   0.978581046389316
1   0.021037927064929   0.978962072935071
19  0.01496138275413    0.985038617245871
15  0.013040629549786   0.986959370450214
10  0.011114480140262   0.988885519859738
12  0.008684188037739   0.991315811962261
MT  1.58665051548522E-05    0.999984133494845

[Ni-Ar]

Hey @luckysardar,

if you're saying that you're running this pipeline on this PGCLC day 5 XGFP- rep 3 sample than I guess the results you get are pretty good.

If I remember correctly only chr X and 13 are fully hybrid with good distribution of the Cas and Mus SNPs. You can check a distribution of the SNPs here. Anyway I'm pinging @Jacq3lin3 and @MoritzBauer (the paper first authors) as they know better.

So the allelic ratio of chr 13 is perfectly 50% and chr9 also very close, while chr X is not reflecting the X chromosome Inactivation (XCI) happening in XGFP- PGLCs.

Nicco

[Ni-Ar]

@lucacozzuto I created a while back a small sh script that counts the sum allele counts per file. I'd like to push it to the development branch but I don't have write access. I'd avoid creating a fork if you agree.

[lucacozzuto]

Yes. Please go ahead

[luckysardar]

Thank you @Ni-Ar @lucacozzuto for the clarification

[Ni-Ar]

Yes. Please go ahead

@lucacozzuto I think that biocoreCRG needs to grant me write access. I'm reading info here.

Cause from my GitHub Desktop I see this message when trying to push to the development branch.

[lucacozzuto]

Strange. You should be able to fork and to make a pull request

[Ni-Ar]

yes I could fork + PR. I wanted (if possible) to commit to the "development" branch directly.