Comments (5)
Hi, please check your python version using python --version
. Currently, NextPolish only support python2.7, I will move it to python3 in the future.
from nextpolish.
Thank you.
My python version is Python 3.7.3 now. I am not sure other software would rely on this version. So, how could I fix this problem?
from nextpolish.
Maybe you can install python2.7 in your personal directory.
from nextpolish.
Thank you so much.
I went through that step. But, new error came out qsub the test task.
"[ERROR] 2019-10-16 20:39:14,367 polish_genome failed: please check the following logs:
[ERROR] 2019-10-16 20:39:14,368 */NextPolish/test_data/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome0/nextPolish.sh.e
[ERROR] 2019-10-16 20:39:14,368 */NextPolish/test_data/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.e"
nextPolish.sh.e* details:
"Traceback (most recent call last):
File "/NextPolish/lib/nextPolish.py", line 83, in
P = CDLL(os.path.dirname(os.path.realpath(file)) + '/' + "nextPolish.so")
File "/NextPolish/lib/python2.7/ctypes/init.py", line 366, in init
self._handle = _dlopen(self._name, mode)
OSError: liblzma.so.5: cannot open shared object file: No such file or directory"
from nextpolish.
It seems your system lacks the Liblzma.so.5 lib, may be you should install it firstly.
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Related Issues (20)
- Need information related to example given in NextPolish Software under the folder test_data HOT 4
- MissAssembly Correction using NextPolish (Need Suggestions) HOT 1
- nextpolish2.py never stop HOT 6
- Adding Hisat2 instead of BWA HOT 1
- error of generate_lqseqs_from_cluster HOT 3
- repeat regions HOT 5
- 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
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