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medema-group / bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
GNU Affero General Public License v3.0
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Trouble querying antiSMASH BGCs #47

Closed pjtorres closed 2 years ago

pjtorres commented 2 years ago

I installed BIGSlice from source and tested it using the input folder and everything works great! I attempted to run some antiSMASH 5.1.1 results through Big Slice. My output file contains the main region.gbk files:

GCF_902388275.1_UHGG_MGYG-HGUT-02545/NZ_LR699017.1.region001.gbk GCF_902388275.1_UHGG_MGYG-HGUT-02545//NZ_LR699017.1.region002.gbk

So I ran the following query: bigslice --query GCF_902388275.1_UHGG_MGYG-HGUT-02545/ --n_ranks 1 out_bigslice_GCF_902388275.1 I get the following error:

Output folder didn't exists!
BiG-SLiCE run failed.

Not sure what is going on. Any tips would be helpful.

satriaphd commented 2 years ago

hi, the "output folder" was supposed to be the result folder that BiG-SLiCE produces. based on your case (tested using the input folder), you haven't run the main part (without --query) of BiG-SLiCE on a big dataset that you want to query on, so I suppose you just wanted to query your BGCs from our pre-calculated results? in that case you can try directly using BiG-FAM (https://bigfam.bioinformatics.nl/query)

ClinicalAI commented 1 year ago

How we can run BiG-Fam on the results of antismash we got in our computer? The Big-Fam website seems just works with antismash job id. Any stand alone version for big-fam?

Caiyulu-818 commented 1 year ago

Hi, I meet the same problem, do you solve this problem? any tips ?