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EvolBioInf / fur

Find Unique genomic Regions
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Can not read fasta files #8

Open 3miumi opened 1 year ago

3miumi commented 1 year ago

Hi,

Thanks for publishing this software. I encountered the problem of reading fasta file. The targets and neighbors are Salmonella enterica but differed from serovar. The sample are all from NCBI reference genome(like). When I try to run makeFurDb, it gives me error about reading FASTA file. Can you please help with this?

Thanks, Ming


makeFurDb -t targets -n neighbors -d furDb
# Reading data...done.
' in sequence on line 4th target representative "targets/GCA_002048395.1_ASM204839v1_genomic.fna"...macle: <stdin>: Unexpected character '
Invalid FASTA file!
haubold commented 1 year ago

Could you please post a sample of the offending file(s)? Thanks, Bernhard.

3miumi commented 1 year ago

Could you please post a sample of the offending file(s)? Thanks, Bernhard.

I have four samples in targets and none of them can be read successfully. They are GCA_000486305.1, GCA_003409095.1,GCA_000806805.1,GCA_002048395.1.

Thanks for your help! Ming

haubold commented 1 year ago

Thanks, I downloaded the four assemblies you list and constructed a tree from them using phylonium and three programs from my biobox: $ phylonium *.fna | nj | midRoot | plotTree tree So I put *805.fna into the directory targets, the other three into the directory neighbors. Then I ran makeFurDb and fur, which worked as expected. I don't know why macle isn't working for you (you did unzip the sequence files?). If you gave me access to your actual input data, I could perhaps take another look.

3miumi commented 1 year ago

Thank you so much for testing it! The files were all unzipped. I installed the software through Docker and using bind mount to create a container (an instance of fox image) in order to access my local host folder. I am not sure if the bind mount may cause the problem. I am quite new with Docker. Do you know if there is any other way that I can run the software on the docker and getting access to host directory? Very appreciated your time!

haubold commented 1 year ago

Did you unzip the data under Windows or Mac? These operating systems use other newline characters than Unix, which might then confuse macle. If that were the case, you could try unzipping the data from inside the Docker container.