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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
43 stars 19 forks source link

ImportError: libhts.so.2: cannot open shared object file: No such file or directory #38

Closed sagitaninta closed 3 years ago

sagitaninta commented 3 years ago

I just tried to get paleomix using conda as instructed in the documentation but this is what I got when running a script independently:

python rmdup_collapsed.py 
Traceback (most recent call last):
 File "rmdup_collapsed.py", line 27, 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 also cannot run the example pipeline

paleomix bam example .
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 have installed htslib manually and include the path at my .bashrc and it still cannot find that libhts.so.2. Could you point a possible solution? Nothing about this on the troubleshooting page. Thanks in advance

MikkelSchubert commented 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:

  1. Is the conda environment active when you try to run python rmdup_collapsed.py?
  2. And what happens if you try to run the script the normal way, namely via 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

sagitaninta commented 3 years ago

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.

  1. Yes the conda environment is active when all of this happened.
  2. Here is the result:
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

MikkelSchubert commented 3 years ago

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

ztang040 commented 3 years ago

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

MikkelSchubert commented 3 years ago

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

ztang040 commented 3 years ago

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

MikkelSchubert commented 3 years ago

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

ztang040 commented 3 years ago

Hi Mikkel,

Thank you for your remind. I would try to run this one now.

Cheers, Zitian

ztang040 commented 3 years ago

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

MikkelSchubert commented 3 years ago

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

ztang040 commented 3 years ago

Sure

(paleomix) [ztang@gruffalo project]$ conda list -n paleomix

packages in environment at /home/ztang/miniconda3/envs/paleomix:

#

Name Version Build Channel

_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:

!/bin/bash

SBATCH --job-name="paleomix"

SBATCH --export=ALL

SBATCH --partition=gpu --mem=16G --cpus-per-task=8

Do some work:

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:

MikkelSchubert commented 3 years ago

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

ztang040 commented 3 years ago

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:

dependencies:

(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

#

To activate this environment, use

#

$ conda activate paleomix

#

To deactivate an active environment, use

#

$ conda deactivate

(base) [ztang@gruffalo ~]$ conda list -n paleomix

packages in environment at /home/ztang/miniconda3/envs/paleomix:

#

Name Version Build Channel

_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.

ztang040 commented 3 years ago

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.