"other entries", "other sequences" raise AttributeError when using --include-children
yeemey opened this issue · 0 comments
yeemey commented
Hello,
When I run extract_kraken_reads.py with --include-children on a kraken2 report that includes "other entries" and "other sequences," I get the following error:
Traceback (most recent call last):
File "/bin/KrakenTools/extract_kraken_reads.py", line 447, in <module>
main()
File "/bin/KrakenTools/extract_kraken_reads.py", line 237, in main
while level_num != (prev_node.level_num + 1):
^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'level_num'
I used print(report_vals)
here and traced the error to having "other entries" and "other sequences" lines in the report in between other taxonomic groups. When I move both "other entries" and "other sequences" to the end of the report, extract_kraken_reads.py runs to completion without errors. I still have to check however, if I've messed up the read extraction by doing that.