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make_sketch() missing required arguments: 'kmer' and 'sketch' #4

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snayfach opened this issue Jan 4, 2021 · 2 comments
Open

make_sketch() missing required arguments: 'kmer' and 'sketch' #4

snayfach opened this issue Jan 4, 2021 · 2 comments

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@snayfach
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snayfach commented Jan 4, 2021

Hello - I've just downloaded the tool and am getting started. Tried a test run but ran into the error below. Adding -k 16 -s 5000 did not solve the issue:

python BiG-MAP/src/BiG-MAP.family.py -p 8 -D bgcs -O test

_Extracting fasta files
Traceback (most recent call last):
File "BiG-MAP/src/BiG-MAP.family.py", line 1219, in
main()
File "BiG-MAP/src/BiG-MAP.family.py", line 1061, in main
make_sketch(args.outdir + os.sep)
TypeError: make_sketch() missing 2 required positional arguments: 'kmer' and 'sketch'

@snayfach
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snayfach commented Jan 4, 2021

Running into several other issues now. For example on ~ line 197:
absolute_loc_start = record.annotations["structured_comment"]["antiSMASH-Data"]["Orig. start"]

However, the "Orig. start" key is not in record.annotations["structured_comment"]["antiSMASH-Data"] for my genbank files. It might be helpful is there were a small test dataset that could be quickly run

@HAugustijn
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BiG-MAP.family takes output produced by antiSMASH/gutSMASH as input. Did you run one of these tools on your genbank files before using them as input for BiG-MAP?

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