lilypeck
lilypeck
Ah right, so not a diamond problem. That is a PASA gff3 file downloaded from mycocosm for a closely-related species, so I could just remove it and re-run. Will report...
Removing the --pasa_gff flag worked, but I am now getting a different error with CodingQuarry. Do you know what might be causing this? Both stringtie.gff3 and genome.softmasked.fa are in /home/lily/funannotate/fun_out/predict_misc...
hi just to update this i used singularity to pull the docker image and everything has worked perfectly
Thank you for your response. It is at this site [https://valleyoak.ucla.edu/genomic-resources/](url) and this link, called `GZIP’d Gene Models, gtf format (~6.3MB)` [https://ucla.box.com/shared/static/rezllcooeeebb8rqmnypkpa9mzgl5k5f.gz](url)
Hi @hhg7, thank you very much, could you resend please as I can't download that file?
Hi @hhg7 Thank you so much, and apologies for my very delayed response. That worked perfectly! Lily
Hello @ArtRand Thank you for your response! I have just checked with v0.2.7 and I don't get the tabix file error - ``` > reading reference FASTA at "/u/home/l/ldpeck/genome_resources/GCF_001633185.2_ValleyOak3.2_genomic.fna" >...
Hello @ArtRand Thank you very much! Tabix is: ``` tabix (htslib) 1.19.1 Copyright (C) 2024 Genome Research Ltd. ``` The complete .bedmethyl is too big to upload, so I have...
Hi @ArtRand Thank you so much it is working now! Lily
Hi @mikolmogorov Thank you, I think you were right about the scaffolding flag. I was also surprised by the total lengths above, as the assembly size is 830 Mb, so...