Mapping to Whole reference genome, ipyrad error step 3

[littlelimia]

Hello all, I am encountering troubles when trying to use a reference genome for mapping in Ipyrad. Please take a look at the error message in the pic. I have never had this issue with a reference genome before, but this one is particularly large. This is the reference I am trying to use ;. I downloaded the .fasta via SRA-toolkit.

Encountered an Error. Message: IPyradError: b'[E::hts_hopen] Failed to open file -\n[E::hts_open_format] Failed to open file "-" : Exec format error\nsamtools sort: can't open "-": Exec format error\n' Parallel connection closed.

I am starting to think that this file is not fully compatible with ipyrad, but I am new at this, so I would appreciate any insights into what might be happening/ways to fix it.

Thank you so much,

Pat

[isaacovercast]

Does it work with different reference genomes? Did you update ipyrad or conda recently? How is the fasta file formatted? Can you show me the first 10-20 lines this fasta file?

[littlelimia]

Thanks for checking in. Yes, I have been able to do it before but this is the first time with such large file. I have not updated in a while.

This is how the first 20 lines of the .fasta file look like.

Thank you,

Pat

[isaacovercast]

Is it an assembled genome? Why are all the sequences 151bp? It looks like raw data? Where did this genome come from?

[littlelimia]

Sorry, I thought I had included the link of the assembly in the first message. Here it is: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR20897177&display=metadata

[isaacovercast]

That looks like the raw data, unassembled illumina reads. You need to find the genome assembly itself, if it has been published already.