Unable to see refgene output
Closed this issue · 1 comments
sparthib commented
Hi, I tried running LIQA on the sample.gtf file,
this was my command:
liqa -task refgene -ref $REFERENCE_GTF -format gtf -out $STEP1_REFGENE/step1.refgene
I see this printed 14 genes are being processed...
But I don't see any output in my resulting refgene file.
This is my environment info.
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
astor 0.8.1 pypi_0 pypi
autograd 1.6.2 pypi_0 pypi
autograd-gamma 0.5.0 pypi_0 pypi
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 pypi_0 pypi
cairo 1.14.12 h80bd089_1005 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge
cycler 0.11.0 pypi_0 pypi
expat 2.5.0 hcb278e6_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonttools 4.38.0 pypi_0 pypi
formulaic 0.6.6 pypi_0 pypi
freetype 2.12.1 h267a509_2 conda-forge
future 0.18.3 pypi_0 pypi
gettext 0.21.1 h27087fc_0 conda-forge
glib 2.56.2 had28632_1001 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphlib-backport 1.0.3 pypi_0 pypi
gsl 2.2.1 h0c605f7_3
harfbuzz 1.9.0 he243708_1001 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
interface-meta 1.3.0 pypi_0 pypi
jpeg 9e h0b41bf4_3 conda-forge
kiwisolver 1.4.5 pypi_0 pypi
krb5 1.16.4 h2fd8d38_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran 3.0.0 1 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libtiff 4.2.0 hf544144_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lifelines 0.27.8 pypi_0 pypi
liqa 1.3.4 pypi_0 pypi
make 4.3 hd18ef5c_1 conda-forge
matplotlib 3.5.3 pypi_0 pypi
ncurses 6.4 h59595ed_2 conda-forge
numpy 1.21.6 pypi_0 pypi
openssl 1.1.1w hd590300_0 conda-forge
packaging 23.2 pypi_0 pypi
pandas 1.3.5 pypi_0 pypi
pango 1.40.14 hf0c64fd_1003 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pillow 9.5.0 pypi_0 pypi
pip 23.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.1.1 pypi_0 pypi
pysam 0.22.0 pypi_0 pypi
python 3.7.3 h5b0a415_0 conda-forge
python-dateutil 2.8.2 pypi_0 pypi
pytz 2023.3.post1 pypi_0 pypi
r-base 3.5.1 h391c2eb_5 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
scipy 1.7.3 pypi_0 pypi
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlite 3.28.0 h8b20d00_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h0c5db8f_5 conda-forge
typing-extensions 4.7.1 pypi_0 pypi
tzdata 2023c h71feb2d_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 pypi_0 pypi
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 1.8.7 h8ee46fc_0 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-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Any pointers would be appreciated, thanks!
-Sowmya
agouru55 commented
Hi, perhaps try running the command with the full directories written out instead of the shortcuts you have above - that can sometimes interfere with the output location. You may also want to ensure that the output directory you are saving to exists. The environment also looks as needed. If the tip above does not work, try reinstalling LIQA via git clone and see if you continue to run into this issue.