Ragout error - TypeError: expected str, bytes or os.PathLike object, not NoneType

[ChuChuChaddy]

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]

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]

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. — Reply to this email directly, view it on GitHub <#76 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHUSONAHAUDB7ZIJBBDPXNTU5Q2T3ANCNFSM5N27USQA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- PhD Student Baylor University Department of Environmental Science