Patch output files still incomplete

[horvathdp]

Help please! I thought I had figured out the problem, but it seems my fix was ineffective. Here is the std error for the patch run:

Wed May 7 15:06:32 2025 --- INFO: Running: ragtag_splitasm.py -o /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.ctg.agp /project/camelina_assemblies/cphasing/ragtag_output/ragtag.scaffold.fasta > /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.ctg.fasta 2> /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.err
Wed May 7 15:11:05 2025 --- INFO: Finished running : ragtag_splitasm.py -o /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.ctg.agp /project/camelina_assemblies/cphasing/ragtag_output/ragtag.scaffold.fasta > /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.ctg.fasta 2> /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.err
Wed May 7 15:11:05 2025 --- INFO: Running: ragtag_rename.py /project/camelina_assemblies/alligatorweed/34.3_50K.fasta -p qseq -o /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.rename.agp > /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.rename.fasta 2> /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.err
Wed May 7 15:11:59 2025 --- INFO: Finished running : ragtag_rename.py /project/camelina_assemblies/alligatorweed/34.3_50K.fasta -p qseq -o /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.rename.agp > /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.rename.fasta 2> /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.err
Wed May 7 15:11:59 2025 --- INFO: Writing: /project/camelina_assemblies/cphasing/ragtag_output/ragtag.patch.comps.fasta
Wed May 7 15:14:03 2025 --- INFO: Mapping the query genome to the target genome
Traceback (most recent call last):
File "/software/el9/apps/ragtag/2.1.0/bin/ragtag_patch.py", line 518, in
main()
File "/software/el9/apps/ragtag/2.1.0/bin/ragtag_patch.py", line 372, in main
al.run_aligner()
File "/software/el9/apps/ragtag/2.1.0/lib/python3.11/site-packages/ragtag_utilities/Aligner.py", line 170, in run_aligner
if all([self.params_are_valid(), self.exec_is_valid()]):
^^^^^^^^^^^^^^^^^^^^
File "/software/el9/apps/ragtag/2.1.0/lib/python3.11/site-packages/ragtag_utilities/Aligner.py", line 116, in exec_is_valid
raise ValueError("The provided aligner executable is not valid: " + self.aligner)
ValueError: The provided aligner executable is not valid: nucmer

[maojanlin]

Hi @horvathdp, I believe it's because you haven't installed nucmer correctly (see the last line error message). Try running nucmer directly in the command line with command like $nucmer --maxmatch -l 100 -c 500 -p ragtag_output/ragtag.patch.asm ragtag_output/ragtag.patch.ctg.fasta ragtag_output/ragtag.patch.rename.fasta to see if there is anything wrong. Another possibility is to add --aligner minimap2 when you run ragtag.py patch, in another word, changing the aligner to circumvent the issue.

[horvathdp]

Awesome! Thanks for the idea. I am trying that now. Dave

…

________________________________ From: Mao-Jan Lin ***@***.***> Sent: Thursday, May 29, 2025 11:45 AM To: malonge/RagTag ***@***.***> Cc: Horvath, David - REE-ARS ***@***.***>; Mention ***@***.***> Subject: Re: [malonge/RagTag] Patch output files still incomplete (Issue #200) [https://avatars.githubusercontent.com/u/22385382?s=20&v=4]maojanlin left a comment (malonge/RagTag#200)<#200 (comment)> Hi @horvathdp<https://github.com/horvathdp>, I believe it's because you haven't installed nucmer correctly (see the last line error message). Try running nucmer directly in the command line with command like $nucmer --maxmatch -l 100 -c 500 -p ragtag_output/ragtag.patch.asm ragtag_output/ragtag.patch.ctg.fasta ragtag_output/ragtag.patch.rename.fasta to see if there is anything wrong. Another possibility is to add --aligner minimap2 when you run ragtag.py patch, in another word, changing the aligner to circumvent the issue. — Reply to this email directly, view it on GitHub<#200 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB6P47HQBIQSYBAT7XS7AZ33A42RNAVCNFSM6AAAAAB4U2BSRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSMJZHE3TQOBVGY>. You are receiving this because you were mentioned.Message ID: ***@***.***> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.