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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Unable to complete an analysis using both protein and rna-seq data #836
Greetings, first of all I want to say thank you for creating this tool, I don't come from a informatics background but I've been trying to understand all these tools through self learning, and well working with it have taught me a few things, I have previously manage to use it to predict genes through protein homology using the OrthoDBV11. So regarding the issue, I am trying to run a new analysis now including RNA-seq data, I suspected a few causes to these problem but I am now pretty sure is related to RAM consumption. Not knowing what else could be causing my computer to hang up, I monitored through htop what was going on and found that as soon as the "re_format_aa_fasta.pl" started it progressively consumes the available RAM until... well it causes the computer to hang up and be unresponsive to anything.
I have been running the analysis using 10 threads, while writing this I restarted the process to do it with 6 instead, to my knowledge this shouldn't work, but I guess I will soon find the answer. On the other hand, do you think there's a way for me to limit the amount of RAM to be used, maybe by editing the script to achieve it?
Note: My computer have 16 GB of RAM, and it is the most high-end computer that we have available.
And just in case this is the last process ran according to the braker.log:
Greetings, first of all I want to say thank you for creating this tool, I don't come from a informatics background but I've been trying to understand all these tools through self learning, and well working with it have taught me a few things, I have previously manage to use it to predict genes through protein homology using the OrthoDBV11. So regarding the issue, I am trying to run a new analysis now including RNA-seq data, I suspected a few causes to these problem but I am now pretty sure is related to RAM consumption. Not knowing what else could be causing my computer to hang up, I monitored through htop what was going on and found that as soon as the "re_format_aa_fasta.pl" started it progressively consumes the available RAM until... well it causes the computer to hang up and be unresponsive to anything.
I have been running the analysis using 10 threads, while writing this I restarted the process to do it with 6 instead, to my knowledge this shouldn't work, but I guess I will soon find the answer. On the other hand, do you think there's a way for me to limit the amount of RAM to be used, maybe by editing the script to achieve it?
Note: My computer have 16 GB of RAM, and it is the most high-end computer that we have available.
And just in case this is the last process ran according to the braker.log:
Tue Jun 11 13:51:55 2024: Running gmetp.pl /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /home/salvatierra/outputs/braker/GeneMark-ETP/etp_config.yaml --workdir /home/salvatierra/outputs/braker/GeneMark-ETP --bam /home/salvatierra/outputs/braker/GeneMark-ETP/etp_data/ --cores 10 --softmask 1>/home/salvatierra/outputs/braker/errors/GeneMark-ETP.stdout 2>/home/salvatierra/outputs/braker/errors/GeneMark-ETP.stderr
Both stdout and stderr are empty.
Thanks in advance.