NoneType path error when trying to run metagenome_from_profile.py from default_config.ini
cberta11 opened this issue · 3 comments
Hello! I am new to CAMISIM and am running into a bit of a roadblock. I am attempting to run metagenome_from_profile.py using the default_config.ini file using the instructions that you gave in the manuel and in #48, however I keep getting:
Below I have attached the error readout with the --debug flag. I also attached the copy of my default_config.ini file as well as the package list from the mamba env in which I am attempting to run CAMISIM on the chance I have the incorrect version of one of the required packages. Any help would be greatly appreciated!
Mamba env package list
(camisim-env2) joeberta@JoesLaptop:/mnt/d/camisim/CAMISIM-1.3$ mamba list
packages in environment at /home/joeberta/miniforge-pypy3/envs/camisim-env2:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.12 h4ab18f5_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
biom-format 2.1.16 py39hd3abc70_1 conda-forge
biopython 1.84 py39hd3abc70_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.2 h4bc722e_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.0 hbb29018_2 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
contourpy 1.2.1 py39h7633fee_0 conda-forge
coreutils 8.25 1 bioconda
curl 8.8.0 he654da7_1 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
ete3 3.1.3 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.53.1 py39hcd6043d_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.80.3 h8a4344b_1 conda-forge
glib-tools 2.80.3 h73ef956_1 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gst-plugins-base 1.24.5 hbaaba92_0 conda-forge
gstreamer 1.24.5 haf2f30d_0 conda-forge
h5py 3.11.0 nompi_py39h24b94d4_102 conda-forge
harfbuzz 8.5.0 hfac3d4d_0 conda-forge
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
icu 73.2 h59595ed_0 conda-forge
importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py39h7633fee_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.8 default_h6ae225f_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgcrypt 1.11.0 h4ab18f5_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libglib 2.80.3 h8a4344b_1 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
libgpg-error 1.50 h4f305b6_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.8 hc9dba70_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.3 ha72fbe1_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.16 hd590300_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h2c5496b_1 conda-forge
libxml2 2.12.7 h4c95cb1_3 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
lxml 5.2.2 py39h8a3eb29_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
matplotlib 3.9.1 py39hf3d152e_0 conda-forge
matplotlib-base 3.9.1 py39hd75cb13_0 conda-forge
mpg123 1.32.6 h59595ed_0 conda-forge
munkres 1.0.7 py_1 bioconda
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
nextflow 24.04.3 hdfd78af_0 bioconda
nspr 4.35 h27087fc_0 conda-forge
nss 3.102 h593d115_0 conda-forge
numpy 2.0.0 py39ha0965c0_0 conda-forge
openjdk 21.0.0 haa376d0_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4ab18f5_1 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39hfc16268_1 conda-forge
pcre2 10.44 h0f59acf_0 conda-forge
pillow 10.4.0 py39h16a7006_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
qt-main 5.15.8 ha2b5568_22 conda-forge
readline 8.2 h8228510_1 conda-forge
scipy 1.13.1 py39haf93ffa_0 conda-forge
setuptools 70.3.0 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py39hd3abc70_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
unicodedata2 15.1.0 py39hd1e30aa_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xkeyboard-config 2.42 h4ab18f5_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.19.2 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Hi,
thank you for your interest in CAMISIM! When you want to create a metagenome from profile using the metagenome_from_profile.py script, you are required to provide a profile with the -p option. Since this is not entirely obvious I added the path to a small test BIOM profile as default option which should "fix" your error if you pull the latest version of CAMISIM. Since you seem to be testing, I recommend using the mini_config.ini instead of the default_config.ini
Thank you for your quick response!
Since originally posting, I tried running metagenomesimulation.py using mini_config.ini as I saw suggested in #69.
However, this raised the "Empty BAM file list in line 106" error as seen in #150 et al. Taking the advice from the submitter in that issue, I created a new mamba envirnonment with basically every dependency I could find mentioned in the user manual and/or issue forum as being necessary:
(No clue if changing from python 3.9 to 3.8 was necessary but that's what that user had and I know v3.10 causes a seperate issue) This appeared to be working, however, I repeatedly saw an error flash by relating to ncursesw:
I saw you mention that this might be an issue in #150, so I wnet ahead and aborted the process to try to proactivly tackle another anticipated issue. Ncursesw does not appear to have a anaconda package, so I just ran:
This appeared to solve the ncursesw library issue, and the "Empty BAM file list in line 106" error was no longer raised during the "Generating gold standard assembly" stage as it had previously and ran all the way through sucessfully.
I tried running metagenome_from_profile.py with the mini_config.ini as you just suggested:
This still raises the same "TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType" but I am going to try constructing a biom profile to feed into it since you are saying it is expecting one.
My end goal is to create 16S rRNA metagenomic profiles that mimic species and abundances commonly found in wastewater samples. I saw reference to 16S with CAMISIM being possible (I think in the user manual or the publication?) but my question is do I just need to pull 16S rRNA nucleotide sequences for each species from NCBI or can I still use full genomes from NCBI and just change some sort of setting to only generate reads from the imaginary rRNA "amplicon" region? Also thank you so much for your work, this program is immensly useful!
Did you pull the latest version of CAMISIM (Since it says "1.3" which is the most recent tagged version, but does not include some later bug fixes)? There is an small example biom profile in the defaults folder (mini.biom) which you can provide with the -p option for testing.
Currently you would need to pull your own 16S rRNA sequences out of the genomes, but there will soon be a metatranscriptomic mode as part of "CAMISIM 2"; you can already have a look at the metat branch. In this mode it might be possible to provide gff files only containing the 16S regions and then just simulate these.