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Gaius-Augustus / BRAKER

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
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.gm_key or make_nt_freq_mat.pl error #775

Open genesrus opened 4 months ago

genesrus commented 4 months ago

Dear Authors,

thank you for all your great work!

I am running Braker3 in ET mode from the latest Docker container, I dowloaded the .gm_key, but I get the error below. The genome is a de-novo assembly. I've also previously run Braker in the same container in ES and ETP mode on the same data with success.

Thank you!

docker run -it --platform linux/amd64 --cpus=100 -v /myfolder/:/myfolder/ teambraker/braker3:latest bash cp /mypath/gm_key_64 ~/.gm_key

braker.pl --genome /mypath/AssemblyDeContaminated3.fa.masked --species=myspecie --bam /mypath/RNA_seqAligned.sortedByCoord.out.bam --softmasking --gff3 --workingdir=/home/jovyan/ --threads 48

ERROR in file /opt/BRAKER/scripts/braker.pl at line 5226 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --sequence=/home/jovyan/genome.fa --ET=/home/jovyan/genemark_hintsfile.gff --cores=48 --gc_donor 0.001 1>/home/jovyan/GeneMark-ET.stdout 2>/home/jovyan/errors/GeneMark-ET.stderr Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --sequence=/home/jovyan/genome.fa --ET=/home/jovyan/genemark_hintsfile.gff --cores=48 --gc_donor 0.001 1>/home/jovyan/GeneMark-ET.stdout 2>/home/jovyan/errors/GeneMark-ET.stderr The most common problem is an expired or not present file ~/.gm_key!

GeneMark-ET.stdout :

​check before the run

​ hard_mask is in the 'auto' mode. hard_mask was set to: 100

​ creat directories

​ commit input data

​ prepare input data report

​ commit training data

​ prepare training data report

​ prepare initial model

​ find GC of sequence

GC 41

​ build initial ET model

running step ET_A running gm.hmm on local multi-core system 238 contigs in list concatenate predictions: /home/jovyan/GeneMark-ET/run/ET_A_1 training level ET_A: /home/jovyan/GeneMark-ET/run/ET_A_1 From 436 loaded 436 and ignored dublications 0 exon no_match match_one match_two Initial 778 5 0 Internal 753 3 0 Terminal 796 4 0 Single 605 0 0 CDS_no_match all short long seq_short seq_long CDS_no_match 2932 2172 760 777189 1136392 Intergenic all between_match seq_match Intergenic: 1603 0 0 error, no valid sequences were found error on call: /opt/ETP/bin/gmes/make_nt_freq_mat.pl --cfg /home/jovyan/GeneMark-ET/run.cfg --section stop_TGA --format TERM_TGA

GeneMark-ET.stderr: empty

braker.log: [...]

​**

​ RUNNING GENEMARK-EX

​**

​ Tue Feb 27 18:51:32 2024: Checking whether file /home/jovyan/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information...

​ Tue Feb 27 18:51:32 2024: Executing GeneMark-ET

​ Tue Feb 27 18:51:32 2024: changing into GeneMark-ET directory /home/jovyan/GeneMark-ET

cd /home/jovyan/GeneMark-ET

​ Tue Feb 27 18:51:32 2024: Executing gmes_petap.pl

/usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --sequence=/home/jovyan/genome.fa --ET=/home/jovyan/genemark_hintsfile.gff --cores=48 --gc_donor 0.001 1>/home/jovyan/GeneMark-ET.stdout 2>/home/jovyan/errors/GeneMark-ET.stderr

KatharinaHoff commented 3 months ago

The gm_key was dropped a while ago. Please pull the latest Docker container/update BRAKER & GeneMark.

genesrus commented 3 months ago

Thank you Katharina. The container was the latest one downloaded the same day, after that I also tried the same run on Galaxy, receiving the same error. I did try the same command with another dataset and it worked. So it should be something in my data that is erroneously categorised as a gm-key error. Thank you.