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DominikBuchner / BOLDigger-commandline

BOLDigger as a commandline tool
MIT License
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BOLD did not respond! Retrying #12

Closed manonbayat closed 2 months ago

manonbayat commented 11 months ago

Hi Dominik!

Since a few days I try to run boldigger-cline on a fasta file containing 638 sequences, and everything works well until the last 10% of the downloading. At the 13/14 batch, I just get this message for hours:

23:17:18: Downloading results.
23:17:18: Parsing html.
23:17:18: BOLD did not respond! Retrying.
23:17:18: Requesting BOLD. This will take a while.
23:17:19: Downloading results.
23:17:19: Parsing html.
23:17:19: BOLD did not respond! Retrying.
23:17:19: Requesting BOLD. This will take a while.
23:17:19: Downloading results.
23:17:19: Parsing html.
23:17:19: BOLD did not respond! Retrying.
23:17:19: Requesting BOLD. This will take a while.

I tried on two different computers, and with different internet connections, but I still get the same error. I don't think this is an error with my fasta file (uploaded below in .txt format). Do you have an idea of what would it be? Thank you very much! Manon

TANGO1_test_COI_OTU_rep.txt

cjfields commented 7 months ago

@manonbayat I had this issue as well, and the error is pretty non-intuitive. It turns out both boldigger versions (GUI and command line) require a 'two-line' FASTA input, more specifically that the sequence line doesn't have line breaks. You can get this using a tool like seqkit or seqtk pretty easily:

seqkit seq -w0 original.fasta > 2line.fasta

Once I had the above boldigger worked quite well.

DominikBuchner commented 2 months ago

Sorry for the late reply. Yes BOLDigger was only able to parse 2-line fasta files.

https://github.com/DominikBuchner/BOLDigger2 will automatically handle this for you :)