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jeffersonfparil / compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R
GNU General Public License v3.0
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assess_specific_genes.nf fails to open ORTHOGROUPS_SINGLE_GENE.NT.treefile #19

Open Keevai09 opened 4 months ago

Keevai09 commented 4 months ago

Hi, I am facing the below mention issue. I have tried to go through the module assess_specific_genes.nf and unable to resolve this on my own and would request your help. I am trying this with the test data provided in github.

"ORTHOGROUPS_SINGLE_GENE.NT.treefile" is generated. but still I am getting the below error.

Define the location of the results of OrthoFinder run, i.e. the most recent output folder. Extract orthologs per gene (Outputs: {GENE}.ortho) Move blast output into a seperate directory to clean-up a bit. Extract gene families (Output: {GENE}.orthocounts) Infer gene family expansion and contraction (Outpus: {GENE}.conex) Failed to open ORTHOGROUPS_SINGLE_GENE.NT.treefile

grep: GSTU13_CAFE_results/Gamma_clade_results.txt: No such file or directory Clean-up. Output: (1/3) {GENE}.ortho (2/3) {GENE}.conex (3/3) BLASTOUT/

jeffersonfparil commented 3 months ago

Hi @Keevai09, Thanks for reporting this issue. I will look into this as this may have been caused by recent changes made to fix the issues of other users. I will start here and probably test another gene just to make sure the error is repeatable across other input genes: https://github.com/jeffersonfparil/compare_genomes/blob/96b9c9ad902e6376d288c5d10a88ed0550e1c0bf/modules/assess_specific_genes.nf#L175.

You may do the same if you have the time as I may not have the time at the moment.

Keevai09 commented 3 months ago

Okay. Thank you @jeffersonfparil. I will test with another gene just to make sure.