Closed linzhl1 closed 2 years ago
I have extracted the sequence which caused the problem and ran it with the command: cctyper q.fa test --prodigal meta -t 4 Here is the result. test-DX2.zip
I am also having a similar problem. Any workarounds available?
Thank you for reporting, and providing a sequence which causes the bug. A workaround for now shuold be to use the --skip_blast argument. I will look into fixing the bug ASAP.
Hi both
The bug is now fixed.
The new fixed version (1.6.4) is published on pip and can be upgraded like this:
python -m pip install cctyper --upgrade
It will be available on conda later today.
Hi, I fed the software with metagenomic datasets but an error was raised as follows:
[2022-06-25 15:58:22] INFO: BLASTing for CRISPR near cas operons Traceback (most recent call last): File "/data/linzhl/anaconda3/envs/cctyper/bin/cctyper", line 95, in
repmatch.run()
File "/data/linzhl/anaconda3/envs/cctyper/lib/python3.8/site-packages/cctyper/blast.py", line 37, in run
self.write_gff()
File "/data/linzhl/anaconda3/envs/cctyper/lib/python3.8/site-packages/cctyper/blast.py", line 369, in write_gff
all_seqs[::2] = cr.repeats
ValueError: attempt to assign sequence of size 36 to extended slice of size 35
This problem only came up in one dataset. Do you know what might be causing this?