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a bytes-like object is required, not 'dict' #141
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Have you fixed the error? I encountered the same issue. |
I did, but not using RagTag. at this point in the RagTag assembly you should have a .agp file. I used the .agp file with agptools (https://github.com/WarrenLab/agptools) to finish the assembly step that kept failing in this step in RagTag. This is what that looks like:
combined.fasta = the original contig assembly fasta file that you put into RagTag this worked decently quickly for me and seemed to have given me a good final scaffold assembly! |
same error |
I got same error: Traceback (most recent call last): |
Not sure if RagTag ever found a fix to this issue, but my fix is in this reply: #141 (comment) |
Thanks, I am going that way but having a hard time installing screed package needed for the agptools :-) I will sort it using bioconda instead of pip I guess |
hello,
I am running ragtag scaffold in order to fill in gaps between contigs using a reference genome. everything seems to run fine up until the very end when I get the error:
raise RuntimeError('Failed : %s > %s 2> %s. Check stderr file for details.' % (" ".join(cmd), out, err))
when I look into ragtag.scaffold.err this is what I get:
the code I am running is as follows:
ragtag.py scaffold --mm2-params '-x asm10' genomic.fa combined.fasta -u
any idea on how to fix this error?
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