Problème pithon dans circlator

IFB Core Cluster
#1

bonjour @team.ifbcorecluster et @team.software,

je voudrais utiliser circlator pour circulariser mes génomes bactériens mais lorsque je lance la commande progcheck pour vérifier si toutes les dépendances sont ok, il semble qu'il y ait un problème avec pithon et 'openpyxl' ... (cf la sortie ci dessous). j'ai de plus la même sortie d'erreur quand je lance la ligne de commande ...
Merci par avance pour votre retour !
Bonne fin de journée

Chloé

srun circlator progcheck
srun: job 14787544 queued and waiting for resources
srun: job 14787544 has been allocated resources
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/circlator", line 57, in
exec('import circlator.tasks.' + task)
File "", line 1, in
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/init.py", line 26, in
from circlator import *
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/tasks/init.py", line 15, in
from circlator.tasks import *
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/tasks/progcheck.py", line 3, in
from circlator import versions
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/versions.py", line 2, in
import openpyxl
ModuleNotFoundError: No module named 'openpyxl'

#2

Il y a un problème sur l'environnement Conda, je vais le réinstaller
.

#3

C'est réglé !

#4

Bonjour @gildaslecorguille,

merci pour votre intervention !
je viens de relancer circlator et il semble qu'il y ait un autre problème :
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/circlator", line 57, in
exec('import circlator.tasks.' + task)
File "", line 1, in
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/init.py", line 26, in
from circlator import *
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/bamfilter.py", line 2, in
import pysam
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pysam/init.py", line 5, in
from pysam.libchtslib import *
ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
srun: error: cpu-node-7: task 0: Exited with exit code 1

merci encore par avance

Chloé

#5

bonjour @gildaslecorguille et @team.software,

je suis désolée de vous relancer sur ce problème mais je ne peux toujours pas utiliser circlator sans la résolution de cet autre problème. la commande progcheck me renvoie la même erreur …
merci par avance de votre intervention !

Chloé

#6

Je regarde ça

#7

Fix :crossed_fingers:

#8

yyyeeessss

merci beaucoup @gildaslecorguille :smiley:

Chloé

#9

mmmmmh je suis désolée @gildaslecorguille :grimacing:

j'ai relancé circlator et viens de voir qu'il crash car il ne connait pas la version de samtools :
External dependencies:
bwa 0.7.17 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/bwa
WARNING: Didn't find canu in path. Looked for:canu
nucmer 3.1 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/nucmer
prodigal 2.6.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/prodigal
Found samtools but couldn't get version.
WARNING: SPAdes version 3.13.0 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.
spades 3.13.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/spades.py

Python version:
3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:36:02)
[GCC 9.3.0]

Python dependencies:
openpyxl 3.0.6 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/openpyxl/init.py
pyfastaq 3.17.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pyfastaq/init.py
pymummer 0.11.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pymummer/init.py
pysam 0.15.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pysam/init.py

les autres dépendances ont l'air ok mais c'est samtools et canu la qui semblent être à l'origine du problème
encore merci de vous repencher une nième fois dessus :slightly_smiling_face:

Chloé

#10

Cette fois, c'est la bonne ! :crossed_fingers:

#11

Bonjour @gildaslecorguille,

je rentre de congés et essaye donc d'essayer mon outil tant attendu ... ça a l'air d'un mauvais scetch je suis désolée mais il crash toujours ...
voici la sortie d'erreur
Step : circlator
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/circlator", line 58, in
exec('circlator.tasks.' + task + '.run()')
File "", line 1, in
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/tasks/all.py", line 74, in run
circlator.versions.get_all_versions(None, raise_error=True, assembler=options.assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/versions.py", line 15, in get_all_versions
external_progs.check_all_progs(verbose=False, raise_error=raise_error, filehandle=filehandle, debug=debug, assembler=assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 105, in check_all_progs
make_and_check_prog(prog, verbose=verbose, raise_error=raise_error, filehandle=filehandle, debug=debug, required=prog==assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 78, in make_and_check_prog
handle_error('Found ' + name + " but couldn't get version.", raise_error=raise_error)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 53, in handle_error
raise Error(message + '\nCannot continue')
circlator.external_progs.Error: Found canu but couldn't get version.
Cannot continue
srun: error: cpu-node-19: task 0: Exited with exit code 1
Mbv-L15762C1 ok
Step 3 : circlator done

et la sortie de progcheck :
Circlator version: 1.5.5

External dependencies:
bwa 0.7.17 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/bwa
Found canu but couldn't get version.
nucmer 3.1 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/nucmer
prodigal 2.6.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/prodigal
Found samtools but couldn't get version.
spades 3.13.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/spades.py

Python version:
3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:36:02)
[GCC 9.3.0]

Python dependencies:
openpyxl 3.0.6 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/openpyxl/init.py
pyfastaq 3.17.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pyfastaq/init.py
pymummer 0.11.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pymummer/init.py
pysam 0.15.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pysam/init.py
WARNING: SPAdes version 3.13.0 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.

encore toutes mes excuses, c'est super frustrant des 2 côtés mais un grand merci d'avance

Chloé

#12

Voici la liste des packages Conda qui viennent avec circulator:

conda list 
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
amos                      3.1.0            py36pl5.22.0_3    bioconda
atk-1.0                   2.36.0               h3371d22_4    conda-forge
bcftools                  1.8                  h4da6232_3    bioconda
bio_assembly_refinement   0.5.1                      py_2    bioconda
bwa                       0.7.17               hed695b0_7    bioconda
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
cairo                     1.16.0            h7979940_1007    conda-forge
canu                      2.1.1                he1b5a44_1    bioconda
certifi                   2020.12.5        py36h5fab9bb_1    conda-forge
chrpath                   0.16              h14c3975_1001    conda-forge
circlator                 1.5.5                      py_2    bioconda
curl                      7.71.1               he644dc0_8    conda-forge
dbus                      1.13.6               hfdff14a_1    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
expat                     2.2.10               h9c3ff4c_0    conda-forge
fontconfig                2.13.1            hba837de_1004    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h516909a_0    conda-forge
gdk-pixbuf                2.42.2               h0c95a7a_2    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.66.7               h9c3ff4c_0    conda-forge
glib-tools                2.66.7               h9c3ff4c_0    conda-forge
gnuplot                   5.4.1                hc654d65_1    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
gst-plugins-base          1.14.5               h0935bb2_2    conda-forge
gstreamer                 1.18.3               h3560a44_0    conda-forge
gtk2                      2.24.33              hab0c2f8_0    conda-forge
harfbuzz                  2.7.4                h5cf4720_0    conda-forge
htslib                    1.7                           0    bioconda
icu                       68.1                 h58526e2_0    conda-forge
jdcal                     1.4.1                      py_0    conda-forge
jellyfish                 0.8.2            py36h8f6f2f9_1    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
k8                        0.2.5                he513fc3_0    bioconda
krb5                      1.17.2               h926e7f8_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
libclang                  11.0.1          default_ha53f305_1    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libdeflate                1.3                  h516909a_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgd                     2.3.0                h47910db_1    conda-forge
libglib                   2.66.7               h1f3bc88_0    conda-forge
libgomp                   9.3.0               h2828fa1_18    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libllvm11                 11.0.1               hf817b99_0    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libpq                     12.3                 hfd2b0eb_3    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
libtiff                   4.2.0                hdc55705_0    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.2.0                h3452ae3_0    conda-forge
libwebp-base              1.2.0                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.10               h72842e0_3    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
minimap2                  2.17                 hed695b0_3    bioconda
mummer                    3.23                          4    bioconda
mysql-common              8.0.22               ha770c72_3    conda-forge
mysql-libs                8.0.22               h935591d_3    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nspr                      4.29                 he1b5a44_1    conda-forge
nss                       3.61                 hb5efdd6_0    conda-forge
openjdk                   11.0.8               hacce0ff_0    conda-forge
openpyxl                  3.0.6              pyhd8ed1ab_0    conda-forge
openssl                   1.1.1i               h7f98852_0    conda-forge
pango                     1.42.4               h80147aa_5    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.22.0.1                      0    conda-forge
perl-app-cpanminus        1.7043               pl5.22.0_0    bioconda
perl-dbi                  1.641                pl5.22.0_0    bioconda
perl-digest-hmac          1.03                 pl5.22.0_1    bioconda
perl-encode-locale        1.05                 pl5.22.0_4    bioconda
perl-exporter-tiny        0.042                         1    bioconda
perl-file-listing         6.04                          0    bioconda
perl-filesys-df           0.92                          1    bioconda
perl-html-parser          3.72                 pl5.22.0_1    bioconda
perl-html-tagset          3.20                 pl5.22.0_1    bioconda
perl-http-cookies         6.01                          0    bioconda
perl-http-daemon          6.01                          0    bioconda
perl-http-date            6.02                 pl5.22.0_1    bioconda
perl-http-message         6.11                          0    bioconda
perl-http-negotiate       6.01                          0    bioconda
perl-io-html              1.001                pl5.22.0_1    bioconda
perl-io-socket-ssl        2.024                         0    bioconda
perl-libwww-perl          6.15                          0    bioconda
perl-list-moreutils       0.428                pl5.22.0_0    bioconda
perl-lwp-mediatypes       6.02                 pl5.22.0_1    bioconda
perl-mime-base64          3.15                 pl5.22.0_0    bioconda
perl-net-http             6.09                          0    bioconda
perl-net-ssleay           1.84                 pl5.22.0_0    bioconda
perl-ntlm                 1.09                          1    bioconda
perl-statistics-descriptive 3.0612                        0    bioconda
perl-test-more            1.001002             pl5.22.0_0    bioconda
perl-threaded             5.26.0                        0    bioconda
perl-uri                  1.71                 pl5.22.0_1    bioconda
perl-www-robotrules       6.02                          0    bioconda
perl-xml-parser           2.44                          4    bioconda
perl-xsloader             0.22                 pl5.22.0_0    bioconda
pip                       21.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
prodigal                  2.6.3                h516909a_2    bioconda
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyfastaq                  3.17.0                     py_2    bioconda
pymummer                  0.11.0                     py_0    bioconda
pysam                     0.15.3           py36hbcae180_3    bioconda
python                    3.6.12          hffdb5ce_0_cpython    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
qt                        5.12.9               h9d6b050_2    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
samtools                  1.7                           1    bioconda
setuptools                49.6.0           py36h5fab9bb_3    conda-forge
spades                    3.13.0                        0    bioconda
sqlite                    3.34.0               h74cdb3f_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_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-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.2.1                h7f98852_0    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-recordproto          1.14.2            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.8                ha95c52a_1    conda-forge

Je t'aurais bien dit de prendre contact avec les auteurs mais il y a déjà plusieurs issues sur ce sujet. Les auteurs ne semblent pas faire de support :confused:

Pour validation, je vais ré-installer les dépendances en me basant sur cette liste :

#13

J'ai installé les versions canu==1.4et samtools==1.3.
Mais j'ai des doutes.