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extract_kraken_reads.py ValueError: invalid literal for int() with base 10: 'tot_lvl' #100

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RieLuc23 opened this issue Sep 27, 2024 · 1 comment

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@RieLuc23
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RieLuc23 commented Sep 27, 2024

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

@RieLuc23
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the header of the combined.report is:

#Number of Samples: 23
#Total Number of Reads: 256890

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