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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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Ragout error - TypeError: expected str, bytes or os.PathLike object, not NoneType #76

Open ChuChuChaddy opened 2 years ago

ChuChuChaddy commented 2 years ago

Since I read the paper for Ragout I've been really excited to use it for my work. I've been trying to improve a genome assembly for tree swallow using a method I found in a paper(1) using Ragout. I included a closely related species (Barn swallow) with a high quality genome and added 12 other bird species with high quality genomes into the hal file.

I ran into the previously mentioned issue with hal2mafMP.py (#60) and worked around this using hal2maf. I'm currently running this in a virtual environment on our cluster for the extra memory (~162GB ram). My new error is posted below and I am unsure how to fix it. I've included my recipe file, pbs script and the debug file from Ragout. Any help would be appreciated! Thank you in advance.

[01:03:44] INFO: Reading contigs file Traceback (most recent call last): File "/home/mansfieldc/privatemodules/my/Ragout/bin/ragout", line 32, in sys.exit(main()) File "/home/mansfieldc/privatemodules/my/Ragout/ragout/main.py", line 295, in main _run_ragout(args) File "/home/mansfieldc/privatemodules/my/Ragout/ragout/main.py", line 197, in _run_ragout target_sequences = read_fasta_dict(synteny_backend.get_target_fasta()) File "/home/mansfieldc/privatemodules/my/Ragout/ragout/parsers/fasta_parser.py", line 40, in read_fasta_dict with open(filename, "rb") as f: TypeError: expected str, bytes or os.PathLike object, not NoneType

Coelho et al., A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

ragout.err.txt ragout_script.txt recipe.txt

mikolmogorov commented 2 years ago

Sorry for the late response! You need to provide a path to the file with contigs in your recipe file. Add the following line: tbicolor.fasta = XXX. Not sure why the error was not properly reported - sorry about that.

ChuChuChaddy commented 2 years ago

No worries! Thank you for the reply. I appreciate your help. I'll let you know how it works out.

On Mon, Feb 28, 2022 at 9:13 PM Mikhail Kolmogorov @.***> wrote:

Sorry for the late response! You need to provide a path to the file with contigs in your recipe file. Add the following line: tbicolor.fasta = XXX. Not sure why the error was not properly reported - sorry about that.

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