Comments (4)
Please check the default python version, NextPolish only works with python 2.7.
from nextpolish.
After the make installation, I changed the hashbang of the nextPolish executable to /data/dp1/local/miniconda3/envs/nextpolish/bin/python
It points to a Python environment created with:
conda create -n nextpolish python=2.7 psutil
(nextpolish) berombau@agro:/data/dp1/public/short-reads$ /data/dp1/local/miniconda3/envs/nextpolish/bin/python --version
Python 2.7.15
(nextpolish) berombau@agro:/data/dp1/public/short-reads$ conda list
# packages in environment at /data/dp1/local/miniconda3/envs/nextpolish:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py27_0 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pip 19.3.1 py27_0 conda-forge
psutil 5.6.7 py27h516909a_0 conda-forge
python 2.7.15 h5a48372_1009 conda-forge
readline 8.0 hf8c457e_0 conda-forge
setuptools 42.0.2 py27_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.33.6 py27_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
from nextpolish.
May be you need change the python
in /data/dp1/public/output/nextpolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome00/nextPolish.sh to /data/dp1/local/miniconda3/envs/nextpolish/bin/python
, or add /data/dp1/local/miniconda3/envs/nextpolish/bin/python
to your environment, so when you run python
, it call the /data/dp1/local/miniconda3/envs/nextpolish/bin/python
.
from nextpolish.
An incorrect version of python was indeed the problem. I solved my error by activating the conda environment and executing the unaltered executable with python directly:
conda activate nextpolish
python {path_to_nextPolish} run.cfg
Thank you for your help!
from nextpolish.
Related Issues (20)
- Empty bin directory after installation? HOT 2
- User defined alignment pipeline for short- and long-reads HOT 2
- [question] combine with medaka or not? HOT 3
- run nextplolish2.py sleep HOT 8
- Ignore the secondary alignment HOT 2
- Test run failed at map_genome: "[gzclose] buffer error" HOT 3
- Installation failure with multiple definition of 'rle_auxtab' HOT 3
- db_split failed: HOT 4
- How does NextPolish polish an assembly with long reads? HOT 1
- make[2]: *** [Makefile:30: bwa] Error 1 错误 HOT 1
- slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT HOT 1
- run fails with long read only in conda env HOT 5
- SLURM out of memory and time... HOT 1
- [main_samview] fail to read the header from "-" HOT 1
- zlib.h not found error HOT 1
- polish_genome failed HOT 1
- problem with NextPolish-CentOS6.9.tgz
- The process of polishing causes a significant decrease in genome size. HOT 8
- During the execution of samtools index, I encountered an error: "invalid option -- '@'" HOT 4
- An error message was encountered while running 00.lgs_polish/04.polish.ref.sh.work/polish_genome01
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