I found a big problem in ntJoin script.

[Shokusei]

Hi, @lcoombe I want to use this software to scaffold the contigs obtained from the other genome assembler. However, after typing the command "test_installation.sh" in the test directory, I found the following error message.

(RSEM) [iceplant4561@at138 tests]$ ./test_installation.sh

• echo 'Running ntJoin...' Running ntJoin...
• ../ntJoin assemble target=scaf.f-f.fa target_weight=1 references=ref.fa reference_weights=2 prefix=f-f_test k=32 w=1000 /lustre7/home/iceplant4561/ntJoin/bin/ntjoin_assemble.py -p f-f_test -n 1 -s scaf.f-f.fa.k32.w1000.tsv -l 1 \ -r "2" -k 32 -g 20 -G 0 -t 1 -m 90 ref.fa.k32.w1000.tsv Traceback (most recent call last): File "/lustre7/home/iceplant4561/ntJoin/bin/ntjoin_assemble.py", line 18, in import pybedtools File "/home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/site-packages/pybedtools/init.py", line 16, in from . import contrib File "/home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/site-packages/pybedtools/contrib/init.py", line 5, in from .intersection_matrix import IntersectionMatrix File "/home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/site-packages/pybedtools/contrib/intersection_matrix.py", line 3, in import sqlite3 File "/home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/sqlite3/init.py", line 57, in from sqlite3.dbapi2 import File "/home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/sqlite3/dbapi2.py", line 27, in from _sqlite3 import ImportError: /home/iceplant4561/anaconda3/envs/RSEM/lib/python3.9/lib-dynload/_sqlite3.cpython-39-x86_64-linux-gnu.so: undefined symbol: sqlite3_errstr make: *** [scaf.f-f.fa.k32.w1000.n1.assigned.scaffolds.fa] Error 1

I have asked my friend about this issue once. He said that I may use the other python object "/anaconda3/pkgs/sqlite-3.32.3-hcee41ef_1/lib/libsqlite3.so".

Considering the above facts, I would like you to solve this problem!

[lcoombe]

Hi @Shokusei,

That looks like an issue with your pybedtools installation, which is a dependency of ntJoin. You can see that because the traceback is related to import pybedtools. It looks like you are using a conda environment, so my best first advice would be to create a fresh conda environment, and install the ntJoin dependencies there (or conda install -c bioconda -c conda-forge ntjoin=1.0.8. You can then see whether pybedtools is working as expected by opening an interactive python session, and trying import pybedtools.

Do follow-up with more information if you have found an issue with ntJoin itself, versus the installation of a dependency.

Thank you for your interest in ntJoin! Lauren

[github-actions[bot]]

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