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gvignolle / FunOrder

The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution – novel tool that allows automated identification of essential genes in a biosynthetic gene clusters (BGC) based solely on genomic data
MIT License
6 stars 3 forks source link

using antiSMASH output #1

Open AnneJRomero opened 2 years ago

AnneJRomero commented 2 years ago

Hi,

I followed the installation instructions and the example usage for generic antiSMASH output. I ran my script but the output folders are empty and I got the following error messages. How can I fix this?

My script: for file in Scaffold*.gbk; do echo $file; sh /scratch/ar14g12/PIPS/funorder/FunOrder-2.0.1/funorder_2.0/funorder_server.sh 30 $file /scratch/ar14g12/PIPS/results/antismash/relax/BBM4/funorder_output ascomycota_db ; done

Error: Scaffold1.region001.gbk File "/scratch/ar14g12/PIPS/funorder/FunOrder-2.0.1/funorder_2.0/genbank_to_fasta_v1.2/genbank_to_fasta.py", line 89 print "You must specify an in_file. Use '-h' for help." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("You must specify an in_file. Use '-h' for help.")? Read sequences and write them to individual files Error: Failed to open filename 'Scaffold1.region001.gbk.fasta' Error: Unable to read sequence 'Scaffold1.region001.gbk.fasta' Died: seqretsplit terminated: Bad value for '-sequence' and no prompt *.fasta

gvignolle commented 2 years ago

Dear AnneJRomero,

The Error you sent states, that genbank_to_fasta.py script did not get an input file. Did you try running funorder_server.sh for a single .gbk file to test it?

The command you sent appears to be correct if the absolute paths are correct. You need to run this command in "from within the antiSMASH output-folder", that is the folder with the *.gbk files.

Best wishes