search

bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
54 stars 13 forks source link

_sqlite3.cpython-310-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2 #124

Closed bsb2014 closed 11 months ago

bsb2014 commented 11 months ago

The error details are:

/home/xxx/miniconda3/bin/share/tigmint-1.2.10-1/bin/tigmint-cut -p8 -w1000 -t0 -m3000 -f filtered_reads.tigmint-long.params.tsv -o final.MHC.ng.filtered_reads.cut500.molecule.size2000.distauto.trim0.window1000.spanauto.breaktigs.fa final.MHC.ng.fa final.MHC.ng.filtered_reads.cut500.molecule.size2000.distauto.bed
Traceback (most recent call last):
  File "/home/xxx/miniconda3/bin/share/tigmint-1.2.10-1/bin/tigmint-cut", line 14, in <module>
    import pybedtools
  File "/home/xxx/miniconda3/lib/python3.10/site-packages/pybedtools/__init__.py", line 16, in <module>
    from . import contrib
  File "/home/xxx/miniconda3/lib/python3.10/site-packages/pybedtools/contrib/__init__.py", line 5, in <module>
    from .intersection_matrix import IntersectionMatrix
  File "/home/xxx/miniconda3/lib/python3.10/site-packages/pybedtools/contrib/intersection_matrix.py", line 3, in <module>
    import sqlite3
  File "/home/xxx/miniconda3/lib/python3.10/sqlite3/__init__.py", line 57, in <module>
    from sqlite3.dbapi2 import *
  File "/home/xxx/miniconda3/lib/python3.10/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
ImportError: /home/xxx/miniconda3/lib/python3.10/lib-dynload/_sqlite3.cpython-310-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2
make: *** [/home/xxx/miniconda3/bin/share/tigmint-1.2.10-1/bin/tigmint-make:343: final.MHC.ng.filtered_reads.cut500.molecule.size2000.distauto.trim0.window1000.spanauto.breaktigs.fa] Error 1

Any suggestions are appreciated.