run fails with long read only in conda env
splaisan opened this issue · 5 comments
Hi
I freshly installed using conda (nextPolish 1.4.1) and edited the shebang line of /opt/miniconda3/envs/nextpolish/bin/nextPolish so that the conda python be used instead of the system python (issue #97) to fix the import issue I had first.
nextPolish run.cfg
Traceback (most recent call last):
File "/opt/miniconda3/envs/nextpolish/bin/nextPolish", line 13, in <module>
from paralleltask import Task
ModuleNotFoundError: No module named 'paralleltask'
edit:
#!/opt/miniconda3/envs/nextpolish/bin/python
# was /usr/bin/env python
nextPolish now executes when --help is used but fails with real data in the local folder
Here are my inputs, they work with medaka or with racon so the files are correct (latest SUP ONT basecalling filtered for 1kb and Q20+).
I modified the example run.cfg present in the doc.
$ cat run.cfg
[General]
job_type = local
job_prefix = nextPolish
task = best
rewrite = yes
deltmp = yes
rerun = 3
parallel_jobs = 6
multithread_jobs = 5
genome = ./bc01_assembly.fasta
genome_size = auto
workdir = ./nextPolish_results
polish_options = -p {multithread_jobs}
[lgs_option]
lgs_fofn = ./lgs.fofn
lgs_options = -min_read_len 1k -max_depth 100
lgs_minimap2_options = -x map-ont
$ cat lgs.fofn
./bc01.fq.gz
$ nextPolish run.cfg
[4060756 INFO] 2023-11-08 13:21:54 NextPolish start...
[4060756 INFO] 2023-11-08 13:21:54 version:1.4.1 logfile:pid4060756.log.info
[4060756 WARNING] 2023-11-08 13:21:54 Re-write workdir
Traceback (most recent call last):
File "/opt/miniconda3/envs/nextpolish/bin/nextPolish", line 554, in <module>
main(args)
File "/opt/miniconda3/envs/nextpolish/bin/nextPolish", line 377, in main
cfg = ConfigParser(args[1][0]).cfg
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/config_parser.py", line 17, in __init__
self._check()
File "/opt/miniconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/config_parser.py", line 163, in _check
self.cfg['genome_size'] = calgs(self.cfg['genome']) if self.cfg['genome_size'] == 'auto' else parse_num_unit(self.cfg['genome_size'])
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/kit.py", line 181, in calgs
calgs = ctypes.CDLL(os.path.dirname(os.path.realpath(__file__)) + '/' + "calgs.so")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/nextpolish/lib/python3.11/ctypes/__init__.py", line 376, in __init__
self._handle = _dlopen(self._name, mode)
^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: /opt/miniconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/calgs.so: ELF load command address/offset not properly aligned
$ cat pid4060756.log.info
[4060756 INFO] 2023-11-08 13:21:54 NextPolish start...
[4060756 INFO] 2023-11-08 13:21:54 version:1.4.1 logfile:pid4060756.log.info
[4060756 WARNING] 2023-11-08 13:21:54 Re-write workdir
My conda env has:
# packages in environment at /opt/miniconda3/envs/nextpolish:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bwa 0.7.17 he4a0461_11 bioconda
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.1 h5eee18b_0
ca-certificates 2023.08.22 h06a4308_0
gdbm 1.18 hd4cb3f1_4
htslib 1.18 h81da01d_0 bioconda
k8 0.2.5 hdcf5f25_4 bioconda
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
libcurl 8.4.0 h251f7ec_0
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_0
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libnghttp2 1.57.0 h2d74bed_0
libssh2 1.10.0 hdbd6064_2
libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge
libuuid 1.41.5 h5eee18b_0
libzlib 1.2.13 hd590300_5 conda-forge
minimap2 2.26 he4a0461_2 bioconda
ncurses 6.4 h6a678d5_0
nextpolish 1.4.1 py311he4a0461_1 bioconda
openssl 3.1.4 hd590300_0 conda-forge
paralleltask 0.1.1 pyhd8ed1ab_0 conda-forge
perl 5.34.0 h5eee18b_2
pip 23.3 py311h06a4308_0
psutil 5.9.0 py311h5eee18b_0
python 3.11.5 h955ad1f_0
readline 8.2 h5eee18b_0
samtools 1.18 h50ea8bc_1 bioconda
setuptools 68.0.0 py311h06a4308_0
sqlite 3.41.2 h5eee18b_0
tk 8.6.12 h1ccaba5_0
tzdata 2023c h04d1e81_0
wheel 0.41.2 py311h06a4308_0
xz 5.4.2 h5eee18b_0
zlib 1.2.13 hd590300_5 conda-forge
thanks for your help
Same problem here. Do you have any solution yet? Thank you!
I am currently running into the same problem . . . would love to hear any potential ideas/fixes. Thanks!!
thanks @moold but I cannot install from source on my server, we really need a conda solution to use the tool as such with conda or include it in some container automatically.
Hi, splaisan
I got the same problem that "OSError: /opt/miniconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/calgs.so: ELF load command address/offset not properly aligned". After I revised the "genome size" from "auto" to "1,000,000,000" (the size of myself genome), the program work well. You could try it.
best.