DiegoSafian

It appears I had a memory problem as the jobs have been running ok since the memory was increased.

Hi, After updating funannotate as you said, I still have same issue. "UnboundLocalError: local variable 'AUGUSTUS_BASE' referenced before assignment" . "new_species.pl --AUGUSTUS_CONFIG_PATH=/nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/reticulata/funannotate/reticulata_predict/predict_misc/ab_initio_parameters/augustus/ --species=BUSCO_reticulata_predict_2779326087 Could not locate command line parameters file:...

Hi, Thanks a lot. By including the script fo Augustus in the PATH, funannotate predict has been running fine and my issue seems to be resolved as Augustus in at...

Hi, I am loving this pipeline. It produces better gene models and a more complete annotation. Thanks!

It appears there is a problem with Augustus. Running `funannotate predict` unit testing Downloading: https://osf.io/te2pf/download?version=1 Bytes: 1489808 8192 [0.55%]16384 [1.10%]24576 [1.65%]32768 [2.20%]40960 [2.75%]49152 [3.30%]57344 [3.85%]65536 [4.40%]73728 [4.95%]81920 [5.50%]90112 [6.05%]98304 [6.60%]106496...

Hi Joe, Thanks for your reply. I followed your advice and updated using python -m pip install git+https://github.com/nextgenusfs/funannotate.git alone and then with a downgraded augustus to 3.4 (3.3.3 did not...

Hi., The problem finally is solved. I just re-installed funnanotate using `conda install funannotate` insted of` conda install -c bioconda funannotate` and that make it. Not idea how.

I had the same problem. check this: https://groups.google.com/g/hic-pro/c/PrX00iA0N1U The data must be ordered like: data ---sample1 ------f1_R1.fastq ------f1_R2.fastq

Thanks for your answer. yes, that is exactly what I meant. Would you say that this would work in species that diverged less than 60 mya?

Hi, Thanks for your response. I am actually running cnmf using the command line (installed pip install cnmf), but I cannot find the way to enable build_ref=True. Do I need...