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AlexOrlek / getNCBImetadata

Retrieves NCBI metadata from nucleotide or biosample accession ids.
MIT License
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/bin/sh: 1: econtact: not found #1

Open aedecano opened 1 year ago

aedecano commented 1 year ago

Getting the error below after running getmetadata.py -a Biosample_accessions.txt -t biosample -o outdir -e myemail@company.co.uk

**retrieving biosample accession metadata from NCBI /bin/sh: 1: econtact: not found

e #this pipeline step produced error unexpected error; exiting**

The "Biosample_accessions.txt" file only contains multiple biosample accession IDs per the instructions and I'm using my staff email for the -e flag.

MengshiGeMoncy commented 4 months ago

Getting the error below after running getmetadata.py -a Biosample_accessions.txt -t biosample -o outdir -e myemail@company.co.uk

**retrieving biosample accession metadata from NCBI /bin/sh: 1: econtact: not found

e #this pipeline step produced error unexpected error; exiting**

The "Biosample_accessions.txt" file only contains multiple biosample accession IDs per the instructions and I'm using my staff email for the -e flag.

Hi aedecano, I also get this error.

Have you solved this problem or used other packages?

jonathho commented 3 months ago

Hi, I managed to get around this by commenting out the following line in getmetadata.py: runsubprocess(['econtact -email %s -tool biosamplemetadatadownload'%str(args.emailaddress)],shell=True)

Cheers!