You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
When executing extract_kraken_reads.py using a combined report (which was generated by combine_kreports.py) and using one concatenated fasta file I get the following error:
extract_kraken_reads.py -k combined.report -s combined.fasta -o outputnew.fasta -t 590 454169 115981 90371 286
PROGRAM START TIME: 09-27-2024 08:03:49
5 taxonomy IDs to parse
>> STEP 1: PARSING KRAKEN FILE FOR READIDS combined.report
0 reads processedTraceback (most recent call last):
File "/teachstor/share/toolsSS24/workspace/Team_LuVi/Lucas/miniconda3/envs/krakentools/bin/extract_kraken_reads.py", line 433, in <module>
main()
File "/teachstor/share/toolsSS24/workspace/Team_LuVi/Lucas/miniconda3/envs/krakentools/bin/extract_kraken_reads.py", line 285, in main
[tax_id, read_id] = process_kraken_output(line)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/teachstor/share/toolsSS24/workspace/Team_LuVi/Lucas/miniconda3/envs/krakentools/bin/extract_kraken_reads.py", line 98, in process_kraken_output
tax_id = int(tax_id)
^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: 'tot_lvl'
What could be the problem?
Thanks
The text was updated successfully, but these errors were encountered:
When executing extract_kraken_reads.py using a combined report (which was generated by combine_kreports.py) and using one concatenated fasta file I get the following error:
What could be the problem?
Thanks
The text was updated successfully, but these errors were encountered: