Closed sagitaninta closed 3 years ago
Hi,
I'll try to look into this tomorrow, but it would be helpful if you could answer a couple of questions:
python rmdup_collapsed.py
?paleomix rmdup_collapsed
?The scripts included in paleomix are generally not meant to be run directly, though the problem you're experiencing is not the kind I would have expected to see.
Cheers, Mikkel
Hi, thanks for your prompt reply. Yeah, the error message is different when it is because I ran it separately, just that it cannot find paleomix module.
paleomix rmdup_collapsed
Traceback (most recent call last):
File "/home/btx638/software/miniconda3/envs/paleomix/bin/paleomix", line 5, in <module>
from paleomix.main import entry_point
File "/home/btx638/software/miniconda3/envs/paleomix/lib/python3.6/site-packages/paleomix/main.py", line 25, in <module>
import pysam
File "/home/btx638/software/miniconda3/envs/paleomix/lib/python3.6/site-packages/pysam/__init__.py", line 5, in <module>
from pysam.libchtslib import *
ImportError: libhts.so.2: cannot open shared object file: No such file or directory
I was looking also at my own dir and found that I have pysam
and libhts.so.2
in multiple env but not sure how to solve it if this is the problem (still in conda activate paleomix
):
find ~/ -name "libhts.so.2"
/home/btx638/software/miniconda3/envs/vep_env/lib/libhts.so.2
/home/btx638/software/miniconda3/pkgs/htslib-1.9-h4da6232_3/lib/libhts.so.2
/home/btx638/software/miniconda3/pkgs/htslib-1.9-ha228f0b_7/lib/libhts.so.2
/home/btx638/software/ensembl-vep/htslib/libhts.so.2
/home/btx638/software/freebayes/SeqLib/htslib/libhts.so.2
/home/btx638/smcpp/lib/libhts.so.2
/home/btx638/htslib/libhts.so.2
find ~/ -name "pysam"
/home/btx638/software/miniconda3/envs/paleomix/lib/python3.6/site-packages/pysam
/home/btx638/software/miniconda3/pkgs/pysam-0.15.3-py37hda2845c_1/lib/python3.7/site-packages/pysam
/home/btx638/software/miniconda3/pkgs/pysam-0.11.2.2-py36_1/lib/python3.6/site-packages/pysam
/home/btx638/software/miniconda3/lib/python3.7/site-packages/pysam
/home/btx638/smcpp/pkgs/pysam-0.11.2.2-py36_1/lib/python3.6/site-packages/pysam
/home/btx638/smcpp/lib/python3.6/site-packages/pysam
Let me know if you need anything else.
Best, Sabhrina
Hi and sorry for the delay.
The problem seems to be caused by breaking changes in some conda packages that aren't handled as such by the package manager, resulting in an non-functional combination of programs and libraries. You have the htslib installed, just not the version that pysam was looking for.
I've attached an updated conda environment file, which should produce a working paleomix environment: paleomix_environment.yaml.gz
The file is zipped because github doesn't allow yaml files to be attached, so you'll have to unzip it first. Also, remember to remove the old conda environment before installing the updated version:
gunzip paleomix_environment.yaml.gz
conda env remove -n paleomix
conda env create -n paleomix -f paleomix_environment.yaml
Please let me know if that also works for you.
Cheers, Mikkel
Hi Mikkel, This ImportError is also an error that I had encountered during my study. I had followed the comment from you above to de-install and re-install paleomix. But the error still exists, Here is the outcome of my script job, which is quite similar to sagitaninta's issue
(paleomix) [ztang@gruffalo project]$ cat slurm-544598.out /var/spool/slurm/job544598/slurm_script: line 10: activate: No such file or directory Traceback (most recent call last): File "/home/ztang/miniconda3/envs/paleomix/bin/paleomix", line 5, in
from paleomix.main import entry_point File "/home/ztang/miniconda3/envs/paleomix/lib/python3.6/site-packages/paleomix/main.py", line 25, in import pysam File "/home/ztang/miniconda3/envs/paleomix/lib/python3.6/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: libhts.so.2: cannot open shared object file: No such file or directory
Could you provide any alternative solvent for this error please? Thanks in advance
Hi, Thank you for letting me know.
Can you try this conda environment file instead? paleomix_environment.yaml.gz
As before, you'll probably need to remove your existing conda environment first:
gunzip paleomix_environment.yaml.gz
conda env remove -n paleomix
conda env create -n paleomix -f paleomix_environment.yaml
Cheers
Hi, Yes I have already finished those before the last attempt for my script. But the error is still the same.
By the way, the file inside this link "https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz" is already "paleomix_environment.yaml" It can be installed smoothly, but it seems didn't make change for this error... I have no idea where the problem is because everything seems well for the environment installation. If you have any idea where is the problem, please give me some hints.
Cheers
Hi,
Just to be clear: The file I attached in my reply to you is different than the first file I attached in my reply to sagitaninta. I should probably have given it a different filename, but unfortunately I did not think that far.
Please try to remove the paleomix_environment.yaml*
files you already have, and follow the instructions above using this file:
https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz
Cheers
Hi Mikkel,
Thank you for your remind. I would try to run this one now.
Cheers, Zitian
Hi Mikkel, I am back. I have re-installed again using your last link, but regret to say the result is the same.
(paleomix) [ztang@gruffalo project]$ sbatch script_paleomix.sh Submitted batch job 544847 (paleomix) [ztang@gruffalo project]$ sacct JobID JobName Partition Account AllocCPUS State ExitCode
544442 paleomix gpu cropdiv-a+ 8 FAILED 1:0 544442.batch batch cropdiv-a+ 8 FAILED 1:0 544442.exte+ extern cropdiv-a+ 8 COMPLETED 0:0 544444 test job medium cropdiv-a+ 1 COMPLETED 0:0 544444.batch batch cropdiv-a+ 1 COMPLETED 0:0 544444.exte+ extern cropdiv-a+ 1 COMPLETED 0:0 544847 paleomix gpu cropdiv-a+ 8 FAILED 1:0 544847.batch batch cropdiv-a+ 8 FAILED 1:0 544847.exte+ extern cropdiv-a+ 8 COMPLETED 0:0
Test job could be completed easily, but when it comes to paleomix script "ImportError: libhts.so.2: cannot open shared object file: No such file or directory" would come again.
Sincerely, Zitian
Hi,
Can you try to run the following command and attach the output?
conda list -n paleomix
Can you also tell me the exactly what your script_paleomix.sh
script does?
Cheers
Sure
(paleomix) [ztang@gruffalo project]$ conda list -n paleomix
#
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.0 anacondar_1
adapterremoval 2.3.1 hb7ba0dd_1 bioconda
bcftools 1.11 h7c999a4_0 bioconda
binutils_impl_linux-64 2.35.1 h193b22a_2 conda-forge
binutils_linux-64 2.35 hc3fd857_29 conda-forge
bowtie2 2.4.2 py36h5202f60_1 bioconda
bwa 0.7.17 hed695b0_7 bioconda
bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
c-ares 1.17.1 h27cfd23_0
ca-certificates 2021.1.19 h06a4308_0
cairo 1.16.0 h7979940_1007 conda-forge
certifi 2020.12.5 py36h06a4308_0
coloredlogs 15.0 pypi_0 pypi
configargparse 1.2.3 pypi_0 pypi
curl 7.71.1 he644dc0_8 conda-forge
fontconfig 2.13.1 hba837de_1004 conda-forge
freetype 2.10.4 h5ab3b9f_0
fribidi 1.0.10 h7b6447c_0
gcc_impl_linux-64 9.3.0 h70c0ae5_18 conda-forge
gcc_linux-64 9.3.0 h7247604_29 conda-forge
gettext 0.19.8.1 h9b4dc7a_1
gfortran_impl_linux-64 9.3.0 hc4a2995_18 conda-forge
gfortran_linux-64 9.3.0 ha1c937c_29 conda-forge
graphite2 1.3.14 h23475e2_0
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 9.3.0 hd87eabc_18 conda-forge
gxx_linux-64 9.3.0 h0d07fa4_29 conda-forge
harfbuzz 2.7.4 h5cf4720_0 conda-forge
htslib 1.11 hd3b49d5_2 bioconda
humanfriendly 9.1 pypi_0 pypi
icu 68.1 h2531618_0
jpeg 9d h36c2ea0_0 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
krb5 1.17.1 h173b8e3_0
ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libdeflate 1.7 h27cfd23_5
libedit 3.1.20191231 h14c3975_1
libev 4.33 h7b6447c_0
libffi 3.3 he6710b0_2
libgcc 7.2.0 h69d50b8_2
libgcc-devel_linux-64 9.3.0 h7864c58_18 conda-forge
libgcc-ng 9.3.0 h2828fa1_18 conda-forge
libgfortran-ng 9.3.0 hff62375_18 conda-forge
libgfortran5 9.3.0 hff62375_18 conda-forge
libglib 2.66.6 h1f3bc88_3 conda-forge
libgomp 9.3.0 h2828fa1_18 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libnghttp2 1.41.0 hf8bcb03_2
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libpng 1.6.37 hbc83047_0
libssh2 1.9.0 h1ba5d50_1
libstdcxx-devel_linux-64 9.3.0 hb016644_18 conda-forge
libstdcxx-ng 9.3.0 h6de172a_18 conda-forge
libtiff 4.1.0 h2733197_1
libuuid 2.32.1 h7f98852_1000 conda-forge
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 h72842e0_3 conda-forge
lz4-c 1.9.3 h2531618_0
make 4.2.1 h1bed415_1
mapdamage2 2.2.1 pyr40_0 bioconda
ncurses 6.2 he6710b0_1
openjdk 8.0.152 h7b6447c_3
openssl 1.1.1i h27cfd23_0
paleomix 1.3.2 pypi_0 pypi
pango 1.42.4 h69149e4_5 conda-forge
pcre 8.44 he6710b0_0
pcre2 10.36 h032f7d1_1 conda-forge
perl 5.26.2 h14c3975_0
picard 2.25.0 0 bioconda
pip 20.3.3 py36h06a4308_0
pixman 0.40.0 h7b6447c_0
pysam 0.11.2.2 py36_1 bioconda
python 3.6.12 hcff3b4d_2
python_abi 3.6 1_cp36m conda-forge
r-assertthat 0.2.1 r40h6115d3f_2 conda-forge
r-backports 1.2.1 r40hcfec24a_0 conda-forge
r-base 4.0.3 hd23ff56_6 conda-forge
r-brio 1.1.1 r40hcfec24a_0 conda-forge
r-callr 3.5.1 r40h142f84f_0 conda-forge
r-cli 2.3.0 r40hc72bb7e_0 conda-forge
r-codetools 0.2_18 r40hc72bb7e_0 conda-forge
r-colorspace 2.0_0 r40h9e2df91_0 conda-forge
r-crayon 1.4.1 r40hc72bb7e_0 conda-forge
r-desc 1.2.0 r40h6115d3f_1003 conda-forge
r-diffobj 0.3.3 r40hcfec24a_0 conda-forge
r-digest 0.6.27 r40h1b71b39_0 conda-forge
r-ellipsis 0.3.1 r40hcdcec82_0 conda-forge
r-evaluate 0.14 r40h6115d3f_2 conda-forge
r-fansi 0.4.2 r40hcfec24a_0 conda-forge
r-farver 2.0.3 r40h0357c0b_1 conda-forge
r-foreach 1.5.1 r40h142f84f_0 conda-forge
r-gam 1.20 r40h580db52_1 conda-forge
r-ggplot2 3.3.3 r40hc72bb7e_0 conda-forge
r-glue 1.4.2 r40hcfec24a_0 conda-forge
r-gtable 0.3.0 r40h6115d3f_3 conda-forge
r-inline 0.3.17 r40hc72bb7e_0 conda-forge
r-isoband 0.2.3 r40h03ef668_0 conda-forge
r-iterators 1.0.13 r40h142f84f_0 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-labeling 0.4.2 r40h142f84f_0 conda-forge
r-lattice 0.20_41 r40hcfec24a_3 conda-forge
r-lifecycle 0.2.0 r40h6115d3f_1 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-mass 7.3_53 r40hcfec24a_0 conda-forge
r-matrix 1.3_2 r40he454529_0 conda-forge
r-mgcv 1.8_33 r40he454529_0 conda-forge
r-munsell 0.5.0 r40h6115d3f_1003 conda-forge
r-nlme 3.1_152 r40h859d828_0 conda-forge
r-pillar 1.4.7 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.2.0 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40h6115d3f_1 conda-forge
r-pkgload 1.1.0 r40h0357c0b_0 conda-forge
r-praise 1.0.0 r40h6115d3f_1004 conda-forge
r-prettyunits 1.1.1 r40h6115d3f_1 conda-forge
r-processx 3.4.5 r40hcfec24a_0 conda-forge
r-ps 1.5.0 r40hcfec24a_0 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h6115d3f_1003 conda-forge
r-rcpp 1.0.6 r40h03ef668_0 conda-forge
r-rcppgsl 0.3.8 r40hc8faad4_0 conda-forge
r-rematch2 2.1.2 r40h6115d3f_1 conda-forge
r-rlang 0.4.10 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40h6115d3f_0 conda-forge
r-testthat 3.0.1 r40h03ef668_0 conda-forge
r-tibble 3.0.6 r40hcfec24a_0 conda-forge
r-utf8 1.1.4 r40hcdcec82_1003 conda-forge
r-vctrs 0.3.6 r40hcfec24a_0 conda-forge
r-viridislite 0.3.0 r40h6115d3f_1003 conda-forge
r-waldo 0.2.3 r40hc72bb7e_0 conda-forge
r-withr 2.4.1 r40hc72bb7e_0 conda-forge
r-zeallot 0.1.0 r40h6115d3f_1002 conda-forge
readline 8.1 h27cfd23_0
ruamel-yaml 0.16.12 pypi_0 pypi
ruamel-yaml-clib 0.2.2 pypi_0 pypi
samtools 1.11 h6270b1f_0 bioconda
sed 4.8 h7b6447c_0
seqtk 1.3 hed695b0_2 bioconda
setproctitle 1.2.2 pypi_0 pypi
setuptools 52.0.0 py36h06a4308_0
sqlite 3.33.0 h62c20be_0
sysroot_linux-64 2.12 h77966d4_13 conda-forge
tbb 2020.3 hfd86e86_0
tk 8.6.10 hbc83047_0
tktable 2.10 h14c3975_0
wheel 0.36.2 pyhd3eb1b0_0
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.2.1 h7f98852_0 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h27cfd23_1007
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.5 h9ceee32_0
The script_paleomix.sh script:
source activate paleomix
paleomix bam run Thibauld_makefile.yaml --jre-option=-Xmx50g
Additionally, just to confirm it, are the updated .yaml document inside like this:
channels:
Hi again,
I am not sure what is going on, but your conda environment appears to be that produced by the original paleomix_environment.yaml
file linked in the the paleomix documentation. For example, you have bowtie 2.4.2, but the version specified in the updated paleomix_environment.yaml
is 2.3.0. More importantly, you have pysam 0.12.2.2, but you should be having 0.16.0. That is what is causing the problem you have.
I've tested with multiple versions of conda/minicona, but I am not able to reproduce this using the latest paleomix_environment.yaml
file.
Can you try running the following and attach the output?
rm -fv paleomix_environment.yaml*
curl -L https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz | gunzip > paleomix_environment.yaml
cat paleomix_environment.yaml
conda env remove -n paleomix
conda env create -n paleomix -f paleomix_environment.yaml
conda list -n paleomix
Cheers
Hi Mikkel,
Thank you for providing me so much help. I had informed from the @gruffalo server staff today that “You should really remove all traces of that install and follow the instructions specific to the cluster. Conda creates hundreds of thousands of files and a lot of data, and were can't afford to back that up (x 150+ users) hence our custom unusual script that ensures scratch space is used for it.” This maybe another reason for my error. And I am going to execute both suggestions from you and him to have a totally re-installation in my workplace.
By the way, these are the outputs of your command:
(base) [ztang@gruffalo ~]$ curl -L https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz | gunzip > paleomix_environment.yaml
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 600 100 600 0 0 1769 0 --:--:-- --:--:-- --:--:-- 1780
100 219 100 219 0 0 410 0 --:--:-- --:--:-- --:--:-- 410
(base) [ztang@gruffalo ~]$ cat paleomix_environment.yaml
channels:
defaults
bioconda
conda-forge
dependencies:
pip
adapterremoval==2.3.1
samtools==1.6
picard==2.24.2
bowtie2==2.3.0
bwa==0.7.17
mapdamage2==2.2.1
pysam==0.16.0
r-base
r-rcpp
r-rcppgsl
r-gam
r-inline
pip:
(base) [ztang@gruffalo ~]$ conda env remove -n paleomix
Remove all packages in environment /home/ztang/miniconda3/envs/paleomix:
(base) [ztang@gruffalo ~]$ conda env create -n paleomix -f paleomix_environment.yaml
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
libgomp-9.3.0 | 377 KB | ############################################################################# | 100%
perl-threaded-5.26.0 | 4 KB | ############################################################################# | 100%
gfortran_impl_linux- | 10.0 MB | ############################################################################# | 100%
libstdcxx-ng-9.3.0 | 4.0 MB | ############################################################################# | 100%
libstdcxx-devel_linu | 14.0 MB | ############################################################################# | 100%
bowtie2-2.3.0 | 11.3 MB | ############################################################################# | 100%
ld_impl_linux-64-2.3 | 627 KB | ############################################################################# | 100%
gfortran_linux-64-9. | 22 KB | ############################################################################# | 100%
pysam-0.16.0 | 2.4 MB | ############################################################################# | 100%
gxx_linux-64-9.3.0 | 22 KB | ############################################################################# | 100%
gcc_linux-64-9.3.0 | 22 KB | ############################################################################# | 100%
r-waldo-0.2.4 | 78 KB | ############################################################################# | 100%
_openmp_mutex-4.5 | 22 KB | ############################################################################# | 100%
libgfortran5-9.3.0 | 2.0 MB | ############################################################################# | 100%
libgcc-ng-9.3.0 | 7.8 MB | ############################################################################# | 100%
gcc_impl_linux-64-9. | 44.6 MB | ############################################################################# | 100%
picard-2.24.2 | 15.9 MB | ############################################################################# | 100%
binutils_impl_linux- | 9.5 MB | ############################################################################# | 100%
libgfortran-ng-9.3.0 | 21 KB | ############################################################################# | 100%
libgcc-devel_linux-6 | 4.0 MB | ############################################################################# | 100%
gxx_impl_linux-64-9. | 10.6 MB | ############################################################################# | 100%
samtools-1.6 | 521 KB | ############################################################################# | 100%
libglib-2.66.7 | 3.0 MB | ############################################################################# | 100%
binutils_linux-64-2. | 22 KB | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/home/ztang/miniconda3/envs/paleomix/bin/python', '-m', 'pip', 'install', '-U', '-r', '/mnt/shared/home/ztang/condaenv.94y52aej.requirements.txt']
Pip subprocess output:
Collecting paleomix==1.3.2
Using cached paleomix-1.3.2-py3-none-any.whl
Requirement already satisfied: pysam>=0.10.0 in ./miniconda3/envs/paleomix/lib/python3.6/site-packages (from paleomix==1.3.2->-r /mnt/shared/home/ztang/condaenv.94y52aej.requirements.txt (line 1)) (0.16.0)
Collecting coloredlogs>=10.0
Using cached coloredlogs-15.0-py2.py3-none-any.whl (45 kB)
Collecting configargparse>=0.13.0
Using cached ConfigArgParse-1.2.3-py3-none-any.whl
Collecting humanfriendly>=9.1
Using cached humanfriendly-9.1-py2.py3-none-any.whl (86 kB)
Collecting ruamel.yaml>=0.16.0
Using cached ruamel.yaml-0.16.12-py2.py3-none-any.whl (111 kB)
Collecting ruamel.yaml.clib>=0.1.2
Using cached ruamel.yaml.clib-0.2.2-cp36-cp36m-manylinux1_x86_64.whl (549 kB)
Collecting setproctitle>=1.1.0
Using cached setproctitle-1.2.2-cp36-cp36m-manylinux1_x86_64.whl (35 kB)
Installing collected packages: ruamel.yaml.clib, humanfriendly, setproctitle, ruamel.yaml, configargparse, coloredlogs, paleomix
Successfully installed coloredlogs-15.0 configargparse-1.2.3 humanfriendly-9.1 paleomix-1.3.2 ruamel.yaml-0.16.12 ruamel.yaml.clib-0.2.2 setproctitle-1.2.2
done
#
#
#
#
(base) [ztang@gruffalo ~]$ conda list -n paleomix
#
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
_r-mutex 1.0.0 anacondar_1
adapterremoval 2.3.1 hb7ba0dd_1 bioconda
binutils_impl_linux-64 2.35.1 hd53bc6c_1
binutils_linux-64 2.35 hc036e67_29
bowtie2 2.3.0 py36_1 bioconda
bwa 0.7.17 hed695b0_7 bioconda
bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
c-ares 1.17.1 h27cfd23_0
ca-certificates 2021.1.19 h06a4308_0
cairo 1.16.0 h7979940_1007 conda-forge
certifi 2020.12.5 py36h06a4308_0
coloredlogs 15.0 pypi_0 pypi
configargparse 1.2.3 pypi_0 pypi
curl 7.71.1 he644dc0_8 conda-forge
fontconfig 2.13.1 hba837de_1004 conda-forge
freetype 2.10.4 h5ab3b9f_0
fribidi 1.0.10 h7b6447c_0
gcc_impl_linux-64 9.3.0 hee54044_17
gcc_linux-64 9.3.0 hf7c3870_29
gettext 0.19.8.1 h9b4dc7a_1
gfortran_impl_linux-64 9.3.0 h27fae32_17
gfortran_linux-64 9.3.0 hf484925_29
graphite2 1.3.14 h23475e2_0
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 9.3.0 h0331030_17
gxx_linux-64 9.3.0 h487584b_29
harfbuzz 2.7.4 h5cf4720_0 conda-forge
humanfriendly 9.1 pypi_0 pypi
icu 68.1 h2531618_0
jpeg 9d h36c2ea0_0 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
krb5 1.17.1 h173b8e3_0
ld_impl_linux-64 2.35.1 h2b15070_1
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libdeflate 1.6 h516909a_0 conda-forge
libedit 3.1.20191231 h14c3975_1
libev 4.33 h7b6447c_0
libffi 3.3 he6710b0_2
libgcc 7.2.0 h69d50b8_2
libgcc-devel_linux-64 9.3.0 hbc86d28_17
libgcc-ng 9.3.0 h9cbead1_17
libgfortran-ng 9.3.0 he4bcb1c_17
libgfortran5 9.3.0 he4bcb1c_17
libglib 2.66.7 h1f3bc88_0 conda-forge
libgomp 9.3.0 h9cbead1_17
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libnghttp2 1.41.0 hf8bcb03_2
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libpng 1.6.37 hbc83047_0
libssh2 1.9.0 h1ba5d50_1
libstdcxx-devel_linux-64 9.3.0 h4e9a861_17
libstdcxx-ng 9.3.0 h2ae2ef3_17
libtiff 4.1.0 h2733197_1
libuuid 2.32.1 h7f98852_1000 conda-forge
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 h72842e0_3 conda-forge
lz4-c 1.9.3 h2531618_0
make 4.2.1 h1bed415_1
mapdamage2 2.2.1 pyr40_0 bioconda
ncurses 6.2 he6710b0_1
openjdk 8.0.152 h7b6447c_3
openssl 1.1.1i h27cfd23_0
paleomix 1.3.2 pypi_0 pypi
pango 1.42.4 h69149e4_5 conda-forge
pcre 8.44 he6710b0_0
pcre2 10.36 h032f7d1_1 conda-forge
perl 5.26.2 h14c3975_0
perl-threaded 5.26.0 0 bioconda
picard 2.24.2 0 bioconda
pip 20.3.3 py36h06a4308_0
pixman 0.40.0 h7b6447c_0
pysam 0.16.0 py36h71d3148_1 bioconda
python 3.6.12 hcff3b4d_2
python_abi 3.6 1_cp36m conda-forge
r-assertthat 0.2.1 r40h6115d3f_2 conda-forge
r-backports 1.2.1 r40hcfec24a_0 conda-forge
r-base 4.0.3 hd23ff56_6 conda-forge
r-brio 1.1.1 r40hcfec24a_0 conda-forge
r-callr 3.5.1 r40h142f84f_0 conda-forge
r-cli 2.3.0 r40hc72bb7e_0 conda-forge
r-codetools 0.2_18 r40hc72bb7e_0 conda-forge
r-colorspace 2.0_0 r40h9e2df91_0 conda-forge
r-crayon 1.4.1 r40hc72bb7e_0 conda-forge
r-desc 1.2.0 r40h6115d3f_1003 conda-forge
r-diffobj 0.3.3 r40hcfec24a_0 conda-forge
r-digest 0.6.27 r40h1b71b39_0 conda-forge
r-ellipsis 0.3.1 r40hcdcec82_0 conda-forge
r-evaluate 0.14 r40h6115d3f_2 conda-forge
r-fansi 0.4.2 r40hcfec24a_0 conda-forge
r-farver 2.0.3 r40h0357c0b_1 conda-forge
r-foreach 1.5.1 r40h142f84f_0 conda-forge
r-gam 1.20 r40h580db52_1 conda-forge
r-ggplot2 3.3.3 r40hc72bb7e_0 conda-forge
r-glue 1.4.2 r40hcfec24a_0 conda-forge
r-gtable 0.3.0 r40h6115d3f_3 conda-forge
r-inline 0.3.17 r40hc72bb7e_0 conda-forge
r-isoband 0.2.3 r40h03ef668_0 conda-forge
r-iterators 1.0.13 r40h142f84f_0 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-labeling 0.4.2 r40h142f84f_0 conda-forge
r-lattice 0.20_41 r40hcfec24a_3 conda-forge
r-lifecycle 0.2.0 r40h6115d3f_1 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-mass 7.3_53 r40hcfec24a_0 conda-forge
r-matrix 1.3_2 r40he454529_0 conda-forge
r-mgcv 1.8_33 r40he454529_0 conda-forge
r-munsell 0.5.0 r40h6115d3f_1003 conda-forge
r-nlme 3.1_152 r40h859d828_0 conda-forge
r-pillar 1.4.7 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.2.0 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40h6115d3f_1 conda-forge
r-pkgload 1.1.0 r40h0357c0b_0 conda-forge
r-praise 1.0.0 r40h6115d3f_1004 conda-forge
r-prettyunits 1.1.1 r40h6115d3f_1 conda-forge
r-processx 3.4.5 r40hcfec24a_0 conda-forge
r-ps 1.5.0 r40hcfec24a_0 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h6115d3f_1003 conda-forge
r-rcpp 1.0.6 r40h03ef668_0 conda-forge
r-rcppgsl 0.3.8 r40hc8faad4_0 conda-forge
r-rematch2 2.1.2 r40h6115d3f_1 conda-forge
r-rlang 0.4.10 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40h6115d3f_0 conda-forge
r-testthat 3.0.1 r40h03ef668_0 conda-forge
r-tibble 3.0.6 r40hcfec24a_0 conda-forge
r-utf8 1.1.4 r40hcdcec82_1003 conda-forge
r-vctrs 0.3.6 r40hcfec24a_0 conda-forge
r-viridislite 0.3.0 r40h6115d3f_1003 conda-forge
r-waldo 0.2.4 r40hc72bb7e_0 conda-forge
r-withr 2.4.1 r40hc72bb7e_0 conda-forge
r-zeallot 0.1.0 r40h6115d3f_1002 conda-forge
readline 8.1 h27cfd23_0
ruamel-yaml 0.16.12 pypi_0 pypi
ruamel-yaml-clib 0.2.2 pypi_0 pypi
samtools 1.6 h9dace67_6 bioconda
sed 4.8 h7b6447c_0
seqtk 1.3 hed695b0_2 bioconda
setproctitle 1.2.2 pypi_0 pypi
setuptools 52.0.0 py36h06a4308_0
sqlite 3.33.0 h62c20be_0
sysroot_linux-64 2.12 h77966d4_13 conda-forge
tbb 2020.3 hfd86e86_0
tk 8.6.10 hbc83047_0
tktable 2.10 h14c3975_0
wheel 0.36.2 pyhd3eb1b0_0
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.2.1 h7f98852_0 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h27cfd23_1007
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.5 h9ceee32_0
Seems the command reached the right result this time. I would continue to test until the problem solved.
Sincerely, Zitian
发件人: Mikkel Schubert notifications@github.com 日期: 星期五, 2021年2月12日 下午1:41 收件人: MikkelSchubert/paleomix paleomix@noreply.github.com 抄送: TANG Zitian Z.Tang-18@sms.ed.ac.uk, Comment comment@noreply.github.com 主题: Re: [MikkelSchubert/paleomix] ImportError: libhts.so.2: cannot open shared object file: No such file or directory (#38) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi again,
I am not sure what is going on, but your conda environment appears to be that produced by the original paleomix_environment.yaml file linked in the the paleomix documentation. For example, you have bowtie 2.4.2, but the version specified in the updated paleomix_environment.yaml is 2.3.0. More importantly, you have pysam 0.12.2.2, but you should be having 0.16.0. That is what is causing the problem you have.
I've tested with multiple versions of conda/minicona, but I am not able to reproduce this using the latest paleomix_environment.yaml file.
Can you try running the following and attach the output?
rm -fv paleomix_environment.yaml*
curl -L https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz | gunzip > paleomix_environment.yaml
cat paleomix_environment.yaml
conda env remove -n paleomix
conda env create -n paleomix -f paleomix_environment.yaml
conda list -n paleomix
Cheers
― You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/MikkelSchubert/paleomix/issues/38#issuecomment-778201331, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AS2BSNU4NBOSJXKFWP4OEV3S6UVV5ANCNFSM4W5D4NXA.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hi Mikkel,
My script is able to run this time.
I think your command has functioned well.
Many thanks.
546081 paleomix gpu cropdiv-a+ 8 RUNNING 0:0
546081.batch batch cropdiv-a+ 8 RUNNING 0:0
546081.exte+ extern cropdiv-a+ 8 RUNNING 0:0
Best wishes,
Zitian
发件人: Mikkel Schubert notifications@github.com 日期: 星期五, 2021年2月12日 下午1:41 收件人: MikkelSchubert/paleomix paleomix@noreply.github.com 抄送: TANG Zitian Z.Tang-18@sms.ed.ac.uk, Comment comment@noreply.github.com 主题: Re: [MikkelSchubert/paleomix] ImportError: libhts.so.2: cannot open shared object file: No such file or directory (#38) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi again,
I am not sure what is going on, but your conda environment appears to be that produced by the original paleomix_environment.yaml file linked in the the paleomix documentation. For example, you have bowtie 2.4.2, but the version specified in the updated paleomix_environment.yaml is 2.3.0. More importantly, you have pysam 0.12.2.2, but you should be having 0.16.0. That is what is causing the problem you have.
I've tested with multiple versions of conda/minicona, but I am not able to reproduce this using the latest paleomix_environment.yaml file.
Can you try running the following and attach the output?
rm -fv paleomix_environment.yaml*
curl -L https://github.com/MikkelSchubert/paleomix/files/5965990/paleomix_environment.yaml.gz | gunzip > paleomix_environment.yaml
cat paleomix_environment.yaml
conda env remove -n paleomix
conda env create -n paleomix -f paleomix_environment.yaml
conda list -n paleomix
Cheers
― You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/MikkelSchubert/paleomix/issues/38#issuecomment-778201331, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AS2BSNU4NBOSJXKFWP4OEV3S6UVV5ANCNFSM4W5D4NXA.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
I just tried to get paleomix using conda as instructed in the documentation but this is what I got when running a script independently:
I also cannot run the example pipeline
I have installed
htslib
manually and include the path at my.bashrc
and it still cannot find thatlibhts.so.2
. Could you point a possible solution? Nothing about this on the troubleshooting page. Thanks in advance