krabapple

At your suggestion I am currently running pipeline D, using the protozoan OrthoDB data set as protein input plus 23 sequence additions from me -- total # of sequences =1,774,003...

The only error files generated as of now ( the script is still running) are these: ``` [sullis02@log-1 braker2_May5_pipelineD_1]$ find . -name "*err" ./errors/find_python3_re.err ./errors/new_species.stderr ./errors/GeneMark-ES.stderr ./errors/find_python3_biopython.err ``` None of...

I notice the slurm file for this batch process contain ProtHint run logging. I am attaching it here [slurm-6461558.zip](https://github.com/Gaius-Augustus/BRAKER/files/6448260/slurm-6461558.zip)

Based on your suggestios our sysadmin killed process 2281719 This immediately produced an output file tmp and another much larger file Spaln/spaln.gff, and then the whole BRAKER pipeline died without...

FYI, the editing worked and in the end this BRAKER pipeline D run did complete, but it generated an implausible number of genes (>75,000, a third of which were located...

No, I did not; I have since abandoned using RNA and protein inputs together. I can't use TSEBRA because running BRAKER in RNA evidence only mode (BRAKER1) fails at the...

Hello, thank you for the suggestion. To help me attempt it, can you clarify the steps? I am confused as to what you mean by the 'success run' and the...

Does that mean it sorts the input bam file when --UTR , --addUTR, or either, are used? It also means that a file used in a --bam= option never needs...

I have not run a 'regular' pipeline with v 2.1.6 yet. I have only run additional pipeline A (several times) and , just once , additional pipeline C (I haven't...

I ran the script for Aug21_1 again, with --useexisting and --nocleanup. None of these files were in output when it finished: traingenes.good.gtf traingenes.good.fa traingenes.good.nr.fa The only files with remotely similar...