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medema-group / BiG-MAP

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

Open snayfach opened 3 years ago

snayfach commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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?