BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Dear author, there is no doubt that this is a very useful and user-friendly software. However, despite this, I have encountered some difficulties and hope to receive your guidance. The specific situation is that I do not have any output results related to AUGUSTUS, which may be due to the deletion of all empty files in the last step. However, what I am not sure about is why my AUGUSTUS output results are empty. My specific code and generated files are as follows:
The error message in errors is:
merge_transcripts_multi_anchored.stderr ：Processing file ~~/augustus.hints.gtf
merge_transcripts_single_anchored.stderr ：Processing file ~~/genemark.f.multi_anchored.gtf
I am looking forward to your reply and wish you a smooth work！
Dear author, there is no doubt that this is a very useful and user-friendly software. However, despite this, I have encountered some difficulties and hope to receive your guidance. The specific situation is that I do not have any output results related to AUGUSTUS, which may be due to the deletion of all empty files in the last step. However, what I am not sure about is why my AUGUSTUS output results are empty. My specific code and generated files are as follows:
code ：
export GENEMARK_PATH="/public/home/lizongtang/software/gmes_linux_64/" export AUGUSTUS_SCRIPTS_PATH="/public/home/lizongtang/miniconda3/envs/Braker/bin/" export AUGUSTUS_CONFIG_PATH="/public/home/lizongtang/miniconda3/envs/Braker/config/" export AUGUSTUS_BIN_PATH="/public/home/lizongtang/miniconda3/envs/Braker/bin/"
/public/home/lizongtang/miniconda3/envs/Braker/bin/braker.pl --species=PHAI --genome=/public/home/lizongtang/01_wenjain/00_genomic/13_NHAI/01_PHAI_EarlGrey/PHAI_summaryFiles/PHAI.softmasked.fasta --softmasking --bam=PHAI_rnaseq.bam --cores=20 --useexisting --gff3 --skip_fixing_broken_genes
generated files： bam_header.map braker.gtf braker.log errors GeneMark-ET genemark_hintsfile.gff genome_header.map hintsfile.gff species what-to-cite.txt
The error message in errors is: merge_transcripts_multi_anchored.stderr ：Processing file ~~/augustus.hints.gtf merge_transcripts_single_anchored.stderr ：Processing file ~~/genemark.f.multi_anchored.gtf
I am looking forward to your reply and wish you a smooth work！