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I converted all .fna files into 1 single .txt file using
cat *.fna >database.txt
and tried running that .txt file as my --rf but that failed
I copied all the following genome names (see below) into 1 txt file and used that as my --rf but still failed
Acetobacter_ghanensis.LargeContigs.fna
Acetobacterium_woodii_DSM_1030.LargeContigs.fna
Acetobacter_pasteurianus_IFO_3283_01.LargeContigs.fna
Acetobacter_senegalensis.LargeContigs.fna
and more...
To the file in Redirect ANI value to stdout #2 I included the path file so /nfs/turbo/lsi-NPDC/D1-folder/Acetobacter.. etc
for each file and use that overall .txt file as my --rf and failed again
Tried using the D1.tar.gz original file as my --rf but that also failed
Could I see an example of a --rf file or could I get guidance on how to use a NCBI prokaryote ref genomes database downloaded into my own pipeline?
Thanks
The text was updated successfully, but these errors were encountered:
rosave9
changed the title
example fo
issues with reference list file
May 27, 2022
Hi
I'm having issues running a reference list I downloaded from: enve-omics.ce.gatech.edu/data/fastani
(I downloaded the D1 dataset).
I open it and turn it into a .txt file and I see this when I open it in text edit:
Then I opened it in command and I see :
Acetobacter_ghanensis.LargeContigs.fna
Acetobacterium_woodii_DSM_1030.LargeContigs.fna
Acetobacter_pasteurianus_IFO_3283_01.LargeContigs.fna
Acetobacter_senegalensis.LargeContigs.fna
etc
So I tried a few things
I converted all .fna files into 1 single .txt file using
cat *.fna >database.txt
and tried running that .txt file as my --rf but that failed
I copied all the following genome names (see below) into 1 txt file and used that as my --rf but still failed
Acetobacter_ghanensis.LargeContigs.fna
Acetobacterium_woodii_DSM_1030.LargeContigs.fna
Acetobacter_pasteurianus_IFO_3283_01.LargeContigs.fna
Acetobacter_senegalensis.LargeContigs.fna
and more...
To the file in Redirect ANI value to stdout #2 I included the path file so /nfs/turbo/lsi-NPDC/D1-folder/Acetobacter.. etc
for each file and use that overall .txt file as my --rf and failed again
Tried using the D1.tar.gz original file as my --rf but that also failed
Could I see an example of a --rf file or could I get guidance on how to use a NCBI prokaryote ref genomes database downloaded into my own pipeline?
Thanks
The text was updated successfully, but these errors were encountered: