An error of running demo: Error in H5Fcreate(file)

[ym-chen]

Hi, I run drop demo with the command: "snakemake --nolock --cores 1". But I got an error like this:

Load packages
Tue Jun 28 10:02:06 2022: Start counting the split reads ...
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00096.1.M_111124_6_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00103.4.M_120208_3_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00106.4.M_120208_5_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00111.2.M_111215_4_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00116.2.M_120131_1_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00126.1.M_111124_8_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00132.2.M_111215_4_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00149.1.M_111124_6_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00150.4.M_120208_7_trunc
Tue Jun 28 10:02:06 2022: Using existing split read counts for sample: HG00176.4.M_120208_2_trunc
Tue Jun 28 10:02:09 2022 : count ranges need to be merged ...
Error in H5Fcreate(file) : HDF5. File accessibility. Unable to open file.
Calls: getSplitReadCountsForAllSamples ... normalize_dump_filepath -> h5createFile -> H5Fcreate
Execution halted
[Tue Jun 28 10:02:22 2022]
Error in rule AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R:
    jobid: 47
    output: /19.drop_test/01.demo/Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-fraser/rawCountsJ.h5, /19.drop_test/01.demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-fraser/gRanges_splitCounts.rds, /19.drop_test/01.demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-fraser/gRanges_NonSplitCounts.rds, /19.drop_test/01.demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-fraser/spliceSites_splitCounts.rds
    log: /19.drop_test/01.demo/.drop/tmp/AS/fraser/01_2_splitReadsMerge.Rds (check log file(s) for error message)

RuleException:
CalledProcessError in line 130 of /tmp/317593.1.b2c_rd_s1.q/tmpomz0rcwa:
Command 'set -euo pipefail;  Rscript --vanilla /19.drop_test/01.demo/.snakemake/scripts/tmprbf0bffw.01_2_countRNA_splitReads_merge.R' returned non-zero exit status 1.
  File "/tmp/317593.1.b2c_rd_s1.q/tmpomz0rcwa", line 130, in __rule_AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R
  File "/home/conda_envs/envs/drop_env2/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-06-28T095445.305461.snakemake.log

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!

[nickhsmith]

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.

[ym-chen]

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.

[ym-chen]

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.

[nickhsmith]

I'm sorry to hear that. Can you please share

1. the DROP version (drop --version)
2. the results of conda list -n drop_env

[ym-chen]

I'm sorry to hear that. Can you please share

1. the DROP version (drop --version)
2. 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

[nickhsmith]

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

• activate it using conda activate drop_test
• try the demo again
  • snakemake -c1

[ym-chen]

• 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?

[ym-chen]

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

• 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.

[nickhsmith]

We have considered porting DROP to nextflow which would help with the deployment, but this is not in our immediate plans.