Closed ym-chen closed 2 years ago
Hello, I couldn't replicate this issue although it could be related to #333
My best suggestion would be to try a fresh run. I have had issues before with HDF5 errors where an R-session or some other program has been stopped and the file link was for some reason still open as a result the reading and writing of a file during a DROP run was disrupted. The other thing I can think of is that you don't have the file access rights for this directory.
Especially for the demo, my brute force suggestion would be to delete the directory Output/processed_data/aberrant_splicing
and try again, or try to use the --force
flag for the snakemake command
snakemake -c1 --force
hopefully that fixes the problem.
Hello, I couldn't replicate this issue although it could be related to #333
My best suggestion would be to try a fresh run. I have had issues before with HDF5 errors where an R-session or some other program has been stopped and the file link was for some reason still open as a result the reading and writing of a file during a DROP run was disrupted. The other thing I can think of is that you don't have the file access rights for this directory.
Especially for the demo, my brute force suggestion would be to delete the directory
Output/processed_data/aberrant_splicing
and try again, or try to use the--force
flag for the snakemake command
snakemake -c1 --force
hopefully that fixes the problem.
Thank you so much. Your answer gave me some inspiration. And I will try your suggestion. Best wishes.
Hello, I couldn't replicate this issue although it could be related to #333
My best suggestion would be to try a fresh run. I have had issues before with HDF5 errors where an R-session or some other program has been stopped and the file link was for some reason still open as a result the reading and writing of a file during a DROP run was disrupted. The other thing I can think of is that you don't have the file access rights for this directory.
Especially for the demo, my brute force suggestion would be to delete the directory
Output/processed_data/aberrant_splicing
and try again, or try to use the--force
flag for the snakemake command
snakemake -c1 --force
hopefully that fixes the problem.
I tried two methods, but they all didn't work. I got the same error. Do you have any other suggestions? I also have tried to build a Singularity container. But it has more problems.
I'm sorry to hear that. Can you please share
drop --version
) conda list -n drop_env
I'm sorry to hear that. Can you please share
- the DROP version (
drop --version
)- the results of
conda list -n drop_env
The version of DROP is 1.1.4. And the result of conda list -n drop_env
is :
# 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
alsa-lib 1.2.6.1 h7f98852_0 conda-forge
amply 0.1.5 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
atk-1.0 2.36.0 h3371d22_4 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
bc 1.07.1 h7f98852_0 conda-forge
bcftools 1.15.1 h0ea216a_0 bioconda
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_10 conda-forge
bioconductor-annotate 1.72.0 r41hdfd78af_0 bioconda
bioconductor-annotationdbi 1.56.1 r41hdfd78af_0 bioconda
bioconductor-annotationhub 3.2.0 r41hdfd78af_0 bioconda
bioconductor-biobase 2.54.0 r41h5c21468_1 bioconda
bioconductor-biocfilecache 2.2.0 r41hdfd78af_0 bioconda
bioconductor-biocgenerics 0.40.0 r41hdfd78af_0 bioconda
bioconductor-biocio 1.4.0 r41hdfd78af_0 bioconda
bioconductor-biocparallel 1.28.3 r41h619a076_0 bioconda
bioconductor-biocversion 3.14.0 r41hdfd78af_0 bioconda
bioconductor-biomart 2.50.0 r41hdfd78af_0 bioconda
bioconductor-biostrings 2.62.0 r41h5c21468_1 bioconda
bioconductor-bsgenome 1.62.0 r41hdfd78af_0 bioconda
bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 r41hdfd78af_4 bioconda
bioconductor-delayedarray 0.20.0 r41h5c21468_1 bioconda
bioconductor-delayedmatrixstats 1.16.0 r41hdfd78af_0 bioconda
bioconductor-deseq2 1.34.0 r41h619a076_1 bioconda
bioconductor-fraser 1.6.1 r41h619a076_0 bioconda
bioconductor-genefilter 1.76.0 r41ha086028_1 bioconda
bioconductor-geneplotter 1.72.0 r41hdfd78af_0 bioconda
bioconductor-genomeinfodb 1.30.0 r41hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.7 r41hdfd78af_1 bioconda
bioconductor-genomicalignments 1.30.0 r41h5c21468_1 bioconda
bioconductor-genomicfeatures 1.46.1 r41hdfd78af_0 bioconda
bioconductor-genomicranges 1.46.1 r41h5c21468_0 bioconda
bioconductor-genomicscores 2.6.0 r41hdfd78af_0 bioconda
bioconductor-hdf5array 1.22.1 r41h5c21468_0 bioconda
bioconductor-interactivedisplaybase 1.32.0 r41hdfd78af_0 bioconda
bioconductor-iranges 2.28.0 r41h5c21468_1 bioconda
bioconductor-keggrest 1.34.0 r41hdfd78af_0 bioconda
bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 bioconda
bioconductor-outrider 1.12.0 r41h619a076_1 bioconda
bioconductor-pcamethods 1.86.0 r41h619a076_1 bioconda
bioconductor-rhdf5 2.38.0 r41h8b353c4_2 bioconda
bioconductor-rhdf5filters 1.6.0 r41h619a076_1 bioconda
bioconductor-rhdf5lib 1.16.0 r41h5c21468_1 bioconda
bioconductor-rhtslib 1.26.0 r41h5c21468_1 bioconda
bioconductor-rsamtools 2.10.0 r41h619a076_1 bioconda
bioconductor-rsubread 2.8.1 r41h5c21468_0 bioconda
bioconductor-rtracklayer 1.54.0 r41hdc01c10_3 bioconda
bioconductor-s4vectors 0.32.3 r41h5c21468_0 bioconda
bioconductor-sparsematrixstats 1.6.0 r41h619a076_1 bioconda
bioconductor-summarizedexperiment 1.24.0 r41hdfd78af_0 bioconda
bioconductor-variantannotation 1.40.0 r41h5c21468_1 bioconda
bioconductor-xvector 0.34.0 r41h5c21468_1 bioconda
bioconductor-zlibbioc 1.40.0 r41h5c21468_1 bioconda
brotlipy 0.7.0 pypi_0 pypi
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.6.15 pypi_0 pypi
cffi 1.15.0 pypi_0 pypi
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 8.1.3 pypi_0 pypi
click-log 0.3.2 pyh9f0ad1d_0 conda-forge
coin-or-cbc 2.10.8 h3786ebc_0 conda-forge
coin-or-cgl 0.60.6 he2f9439_0 conda-forge
coin-or-clp 1.17.6 h256e9bb_3 conda-forge
coin-or-osi 0.108.7 h3b589db_0 conda-forge
coin-or-utils 2.11.6 h573740c_0 conda-forge
coincbc 2.10.8 0_metapackage conda-forge
configargparse 1.5.3 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
cryptography 37.0.2 pypi_0 pypi
curl 7.83.1 h7bff187_0 conda-forge
datrie 0.8.2 pypi_0 pypi
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
docutils 0.18.1 pypi_0 pypi
dpath 2.0.6 pypi_0 pypi
drop 1.1.4 pyhdfd78af_0 bioconda
expat 2.4.8 h27087fc_0 conda-forge
filelock 3.7.1 pyhd8ed1ab_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 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gatk4 4.2.6.1 py36hdfd78af_1 bioconda
gcc_impl_linux-64 10.3.0 hf2f2afa_16 conda-forge
gcc_linux-64 10.3.0 hc39de41_10 conda-forge
gdk-pixbuf 2.42.8 hff1cb4f_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 10.3.0 h73f4979_16 conda-forge
gfortran_linux-64 10.3.0 hb09a455_10 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
gitpython 3.1.27 pyhd8ed1ab_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 4.0.0 h5abf519_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gtk2 2.24.33 h90689f9_2 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
gxx_impl_linux-64 10.3.0 hf2f2afa_16 conda-forge
gxx_linux-64 10.3.0 h2593f52_10 conda-forge
harfbuzz 4.3.0 hf9f4e7c_0 conda-forge
htslib 1.15.1 h9753748_0 bioconda
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 pypi_0 pypi
importlib_resources 5.8.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
jpeg 9e h166bdaf_1 conda-forge
jsonschema 4.6.0 pyhd8ed1ab_0 conda-forge
jupyter-core 4.10.0 pypi_0 pypi
jupyter_core 4.10.0 py310hff52083_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libcups 2.3.3 hf5a7f15_1 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 10.3.0 he6cfe16_16 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgd 2.3.3 h18fbbfe_3 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libgit2 1.4.3 h6529ace_0 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.2 h7f98852_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
liblapacke 3.9.0 15_linux64_openblas conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
librsvg 2.54.3 h7abd40a_0 conda-forge
libsanitizer 10.3.0 h26c7422_16 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 10.3.0 he6cfe16_16 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.4.0 h0fcbabc_0 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.14 h22db469_0 conda-forge
libzlib 1.2.12 h166bdaf_1 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.1.1 pypi_0 pypi
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.22.4 pypi_0 pypi
openjdk 11.0.15 hc6918da_0 conda-forge
openssl 1.1.1o h166bdaf_0 conda-forge
pandas 1.4.2 pypi_0 pypi
pandoc 2.18 ha770c72_0 conda-forge
pango 1.50.7 hbd2fdc8_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pip 22.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
plac 1.3.5 pyhd8ed1ab_0 conda-forge
psutil 5.9.1 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulp 2.6.0 pypi_0 pypi
py 1.11.0 pyh6c4a22f_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 pypi_0 pypi
pysocks 1.7.1 pypi_0 pypi
python 3.10.5 h582c2e5_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.15.3 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 pypi_0 pypi
r-askpass 1.1 r41hcfec24a_2 conda-forge
r-assertthat 0.2.1 r41hc72bb7e_2 conda-forge
r-backports 1.4.1 r41hcfec24a_0 conda-forge
r-base 4.1.3 h06d3f91_1 conda-forge
r-base64enc 0.1_3 r41hcfec24a_1004 conda-forge
r-bbmisc 1.12 r41h06615bd_0 conda-forge
r-bh 1.78.0_0 r41hc72bb7e_0 conda-forge
r-biocmanager 1.30.18 r41hc72bb7e_0 conda-forge
r-bit 4.0.4 r41hcfec24a_0 conda-forge
r-bit64 4.0.5 r41hcfec24a_0 conda-forge
r-bitops 1.0_7 r41hcfec24a_0 conda-forge
r-blob 1.2.3 r41hc72bb7e_0 conda-forge
r-brew 1.0_7 r41hc72bb7e_0 conda-forge
r-brio 1.1.3 r41hcfec24a_0 conda-forge
r-bslib 0.3.1 r41hc72bb7e_0 conda-forge
r-cachem 1.0.6 r41hcfec24a_0 conda-forge
r-callr 3.7.0 r41hc72bb7e_0 conda-forge
r-catools 1.18.2 r41h03ef668_0 conda-forge
r-checkmate 2.1.0 r41h06615bd_0 conda-forge
r-cli 3.3.0 r41h7525677_0 conda-forge
r-clipr 0.8.0 r41hc72bb7e_0 conda-forge
r-cluster 2.1.3 r41h8da6f51_0 conda-forge
r-codetools 0.2_18 r41hc72bb7e_0 conda-forge
r-colorspace 2.0_3 r41h06615bd_0 conda-forge
r-commonmark 1.8.0 r41h06615bd_0 conda-forge
r-covr 3.5.1 r41h03ef668_0 conda-forge
r-cowplot 1.1.1 r41hc72bb7e_0 conda-forge
r-cpp11 0.4.2 r41hc72bb7e_0 conda-forge
r-crayon 1.5.1 r41hc72bb7e_0 conda-forge
r-credentials 1.3.2 r41hc72bb7e_0 conda-forge
r-crosstalk 1.2.0 r41hc72bb7e_0 conda-forge
r-curl 4.3.2 r41hcfec24a_0 conda-forge
r-data.table 1.14.2 r41hcfec24a_0 conda-forge
r-dbi 1.1.3 r41hc72bb7e_0 conda-forge
r-dbplyr 2.2.0 r41hc72bb7e_0 conda-forge
r-dendextend 1.15.2 r41hc72bb7e_0 conda-forge
r-desc 1.4.1 r41hc72bb7e_0 conda-forge
r-devtools 2.4.3 r41hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r41hcfec24a_0 conda-forge
r-digest 0.6.29 r41h03ef668_0 conda-forge
r-dplyr 1.0.9 r41h7525677_0 conda-forge
r-dt 0.23 r41hc72bb7e_0 conda-forge
r-egg 0.4.5 r41hc72bb7e_2 conda-forge
r-ellipsis 0.3.2 r41hcfec24a_0 conda-forge
r-evaluate 0.15 r41hc72bb7e_0 conda-forge
r-extradistr 1.9.1 r41h03ef668_0 conda-forge
r-fansi 1.0.3 r41h06615bd_0 conda-forge
r-farver 2.1.0 r41h03ef668_0 conda-forge
r-fastmap 1.1.0 r41h03ef668_0 conda-forge
r-filelock 1.0.2 r41hcfec24a_1002 conda-forge
r-fontawesome 0.2.2 r41hc72bb7e_0 conda-forge
r-foreach 1.5.2 r41hc72bb7e_0 conda-forge
r-formatr 1.12 r41hc72bb7e_0 conda-forge
r-fs 1.5.2 r41h7525677_1 conda-forge
r-futile.logger 1.4.3 r41hc72bb7e_1003 conda-forge
r-futile.options 1.0.1 r41hc72bb7e_1002 conda-forge
r-gclus 1.3.2 r41hc72bb7e_2 conda-forge
r-generics 0.1.2 r41hc72bb7e_0 conda-forge
r-gert 1.5.0 r41h30f61c7_1 conda-forge
r-ggplot2 3.3.6 r41hc72bb7e_0 conda-forge
r-ggrepel 0.9.1 r41h03ef668_0 conda-forge
r-ggthemes 4.2.4 r41hc72bb7e_0 conda-forge
r-gh 1.3.0 r41hc72bb7e_0 conda-forge
r-git2r 0.30.1 r41h96773ce_0 conda-forge
r-gitcreds 0.1.1 r41hc72bb7e_0 conda-forge
r-glue 1.6.2 r41h06615bd_0 conda-forge
r-gplots 3.1.3 r41hc72bb7e_0 conda-forge
r-gridextra 2.3 r41hc72bb7e_1003 conda-forge
r-gtable 0.3.0 r41hc72bb7e_3 conda-forge
r-gtools 3.9.2.2 r41h06615bd_0 conda-forge
r-heatmaply 1.3.0 r41hc72bb7e_0 conda-forge
r-hexbin 1.28.2 r41h8da6f51_0 conda-forge
r-highr 0.9 r41hc72bb7e_0 conda-forge
r-hms 1.1.1 r41hc72bb7e_0 conda-forge
r-htmltools 0.5.2 r41h03ef668_0 conda-forge
r-htmlwidgets 1.5.4 r41hc72bb7e_0 conda-forge
r-httpuv 1.6.5 r41h03ef668_0 conda-forge
r-httr 1.4.3 r41hc72bb7e_0 conda-forge
r-ini 0.3.1 r41hc72bb7e_1003 conda-forge
r-isoband 0.2.5 r41h03ef668_0 conda-forge
r-iterators 1.0.14 r41hc72bb7e_0 conda-forge
r-jquerylib 0.1.4 r41hc72bb7e_0 conda-forge
r-jsonlite 1.8.0 r41h06615bd_0 conda-forge
r-kernsmooth 2.23_20 r41h742201e_0 conda-forge
r-knitr 1.39 r41hc72bb7e_0 conda-forge
r-labeling 0.4.2 r41hc72bb7e_1 conda-forge
r-lambda.r 1.2.4 r41hc72bb7e_1 conda-forge
r-later 1.2.0 r41h03ef668_0 conda-forge
r-lattice 0.20_45 r41hcfec24a_0 conda-forge
r-lazyeval 0.2.2 r41hcfec24a_2 conda-forge
r-lifecycle 1.0.1 r41hc72bb7e_0 conda-forge
r-locfit 1.5_9.5 r41h06615bd_0 conda-forge
r-magrittr 2.0.3 r41h06615bd_0 conda-forge
r-mass 7.3_57 r41h06615bd_0 conda-forge
r-matrix 1.4_1 r41h0154571_0 conda-forge
r-matrixstats 0.62.0 r41h06615bd_0 conda-forge
r-memoise 2.0.1 r41hc72bb7e_0 conda-forge
r-mgcv 1.8_40 r41h0154571_0 conda-forge
r-mime 0.12 r41hcfec24a_0 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1004 conda-forge
r-nlme 3.1_158 r41h8da6f51_0 conda-forge
r-openssl 2.0.2 r41hfaab4ff_0 conda-forge
r-pheatmap 1.0.12 r41hc72bb7e_2 conda-forge
r-pillar 1.7.0 r41hc72bb7e_0 conda-forge
r-pkgbuild 1.3.1 r41hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_1 conda-forge
r-pkgload 1.2.4 r41h03ef668_0 conda-forge
r-plogr 0.2.0 r41hc72bb7e_1003 conda-forge
r-plotly 4.10.0 r41hc72bb7e_0 conda-forge
r-plyr 1.8.7 r41h7525677_0 conda-forge
r-png 0.1_7 r41hcfec24a_1004 conda-forge
r-praise 1.0.0 r41hc72bb7e_1005 conda-forge
r-prettyunits 1.1.1 r41hc72bb7e_1 conda-forge
r-processx 3.6.1 r41h06615bd_0 conda-forge
r-progress 1.2.2 r41hc72bb7e_2 conda-forge
r-promises 1.2.0.1 r41h03ef668_0 conda-forge
r-prroc 1.3.1 r41hc72bb7e_1003 conda-forge
r-ps 1.7.1 r41h06615bd_0 conda-forge
r-purrr 0.3.4 r41hcfec24a_1 conda-forge
r-qap 0.1_1 r41h859d828_1006 conda-forge
r-r.methodss3 1.8.2 r41hc72bb7e_0 conda-forge
r-r.oo 1.25.0 r41hc72bb7e_0 conda-forge
r-r.utils 2.11.0 r41hc72bb7e_0 conda-forge
r-r6 2.5.1 r41hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r41hcfec24a_0 conda-forge
r-rcmdcheck 1.4.0 r41h785f33e_0 conda-forge
r-rcolorbrewer 1.1_3 r41h785f33e_0 conda-forge
r-rcpp 1.0.8.3 r41h7525677_0 conda-forge
r-rcpparmadillo 0.11.2.0.0 r41h9f5de39_0 conda-forge
r-rcurl 1.98_1.7 r41h06615bd_0 conda-forge
r-registry 0.5_1 r41hc72bb7e_2 conda-forge
r-rematch2 2.1.2 r41hc72bb7e_1 conda-forge
r-remotes 2.4.2 r41hc72bb7e_0 conda-forge
r-reshape2 1.4.4 r41h03ef668_1 conda-forge
r-restfulr 0.0.14 r41h73dbb54_0 bioconda
r-rex 1.2.1 r41hc72bb7e_0 conda-forge
r-rjson 0.2.21 r41h7525677_1 conda-forge
r-rlang 1.0.2 r41h7525677_0 conda-forge
r-rmarkdown 2.14 r41hc72bb7e_0 conda-forge
r-roxygen2 7.2.0 r41h7525677_0 conda-forge
r-rprojroot 2.0.3 r41hc72bb7e_0 conda-forge
r-rsqlite 2.2.8 r41h03ef668_0 conda-forge
r-rstudioapi 0.13 r41hc72bb7e_0 conda-forge
r-rversions 2.1.1 r41hc72bb7e_0 conda-forge
r-sass 0.4.1 r41h7525677_0 conda-forge
r-scales 1.2.0 r41hc72bb7e_0 conda-forge
r-seriation 1.3.5 r41h8da6f51_0 conda-forge
r-sessioninfo 1.2.2 r41hc72bb7e_0 conda-forge
r-shiny 1.7.1 r41h785f33e_0 conda-forge
r-snow 0.4_4 r41hc72bb7e_0 conda-forge
r-sourcetools 0.1.7 r41h03ef668_1002 conda-forge
r-stringi 1.7.6 r41h30a9eb7_2 conda-forge
r-stringr 1.4.0 r41hc72bb7e_2 conda-forge
r-survival 3.3_1 r41h06615bd_0 conda-forge
r-sys 3.4 r41hcfec24a_0 conda-forge
r-testthat 3.1.4 r41h7525677_0 conda-forge
r-tibble 3.1.7 r41h06615bd_0 conda-forge
r-tidyr 1.2.0 r41h03ef668_0 conda-forge
r-tidyselect 1.1.2 r41hc72bb7e_0 conda-forge
r-tinytex 0.40 r41hc72bb7e_0 conda-forge
r-tmae 1.0.4 r41h9ee0642_0 bioconda
r-tsp 1.2_0 r41h06615bd_0 conda-forge
r-usethis 2.1.6 r41hc72bb7e_0 conda-forge
r-utf8 1.2.2 r41hcfec24a_0 conda-forge
r-vctrs 0.4.1 r41h7525677_0 conda-forge
r-vgam 1.1_6 r41h859d828_0 conda-forge
r-viridis 0.6.2 r41hc72bb7e_0 conda-forge
r-viridislite 0.4.0 r41hc72bb7e_0 conda-forge
r-waldo 0.4.0 r41hc72bb7e_0 conda-forge
r-webshot 0.5.3 r41hc72bb7e_0 conda-forge
r-whisker 0.4 r41hc72bb7e_1 conda-forge
r-withr 2.5.0 r41hc72bb7e_0 conda-forge
r-xfun 0.31 r41h7525677_0 conda-forge
r-xml 3.99_0.10 r41h06615bd_0 conda-forge
r-xml2 1.3.3 r41h7525677_1 conda-forge
r-xopen 1.0.0 r41hc72bb7e_1003 conda-forge
r-xtable 1.8_4 r41hc72bb7e_3 conda-forge
r-yaml 2.3.5 r41h06615bd_0 conda-forge
r-zip 2.2.0 r41hcfec24a_0 conda-forge
ratelimiter 1.2.0 py_1002 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.0 pyhd8ed1ab_0 conda-forge
retry 0.9.2 py_0 conda-forge
samtools 1.15.1 h1170115_0 bioconda
sed 4.8 he412f7d_0 conda-forge
setuptools 62.5.0 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
smart_open 6.0.0 pyhd8ed1ab_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snakemake-minimal 7.8.2 pyhdfd78af_0 bioconda
sqlite 3.38.5 h4ff8645_0 conda-forge
star 2.7.10a h9ee0642_0 bioconda
stopit 1.1.2 py_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tabulate 0.8.9 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toposort 1.7 pyhd8ed1ab_0 conda-forge
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.2.0 pyha770c72_1 conda-forge
tzdata 2022a h191b570_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wbuild 1.8.0 pyhdfd78af_1 bioconda
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.14.1 pypi_0 pypi
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 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 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 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yte 1.5.1 pypi_0 pypi
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_1 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge
In a short-term effort to fix this can you please try this with the linked DROP.yaml
file. It is a yaml file for a conda env called drop_test
DROP.yaml
Can you please try to install it using (~10 min)
conda env create -f DROP.yaml
conda activate drop_test
snakemake -c1
- snakemake -c1
I have tried your suggestion. Only the BSgenome.Hsapiens.UCSC.hg19 package, I used the local installation method. Everything else was installed as you suggested. But unfortunately, I got the same error again. I can successfully run the demo on a server fot testing which is using the Ubuntu system. But it keeps failing when I test on Centos7 server. I wonder if the error may be due to the system reasons?
In a short-term effort to fix this can you please try this with the linked
DROP.yaml
file. It is a yaml file for a conda env calleddrop_test
DROP.yamlCan you please try to install it using (~10 min)
conda env create -f DROP.yaml
- activate it using
conda activate drop_test
try the demo again
snakemake -c1
Hi, good news. I have a right drop_env conda environment. This environment is installed with the same command with mine. So I think there must be some error caused by unstable network when I installed Drop, which eventually led to the error. My own installation is still unsuccessful, but I can use Drop to analyze my data. Thank you very much for your patient help. Your reply gave me a deeper understanding of DROP. And will you consider providing docker or singularity images in the future? I think this will be more convenient.
We have considered porting DROP to nextflow which would help with the deployment, but this is not in our immediate plans.
Hi, I run drop demo with the command: "snakemake --nolock --cores 1". But I got an error like this:
I found some infomation in Google, but they can't work. What's the reason of this HDF5 error? And how can I solve this problem? Thank you for your help!