Nadia Davidson

Hi, Yes you can only pass one de novo assembly file to necklace, but a simple way to get around this is to join all the assemblies into one file....

Hi, did you put quotes around the file name? Can you send the parameter you set?

Hi, Can you try uncommenting the de_novo_assembly_file part in your config file: // sequencing data reads_R1="SRR_1.fastq" reads_R2="SRR_2.fastq” de_novo_assembly_file="all_assemblies.fasta” //The genome and annotation genome=“GCA_000genomic.fa” //The genome and annotation of a related...

No I've never seen an error like this before, justt o confirm, did you run the full command (including the bpipe at the start?) /users/sf6/data/necklace-1.11/tools/bin/bpipe run /sf6/data/necklace-1.11/necklace.groovy necklace.txt What happens...

Did you put quotes around the filename, ie. "assemblies.fasta" in the config file? I just realised I had left these off in the wiki instructions, so apologies for that. Quotes...

Hmm, the variables all need to be on their own line in the config file (not one line). The "//" means it's a comment, so the code will interpret everything...

That's strange, I haven't encountered an error like that before. Is that the full error that was printed? What command do you run? What system are you running on? Are...

Wow... glad you finally found it. How frustrating. The next error is much simpler. Just gzip your fastq files and it should be happy.

Thanks for brining this to my attention. I will have a look at this when I address you other issue. You are also welcome to submit a pull request with...

Hi, can you please send a small toy example that reproduces the issue and I can have a look?