gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.

agmpo commented 11 months ago

I hit a prodigal error while trying to run (many) assemblies. I know this is a lot of genomes I don't think it is running out of RAM because it completed the prodigal step on this file set in a previous run, and the resource usage monitor doesn't indicate anything is out of order. I also have enough space in my account on the server I'm using to write all the files. I swapped from an older version of GTDB-TK to the newest one, checked the .gz files are not corrupt using gzip -t, and changed the fasta headers in all files to unique values (filename_# for each contig). Before changing the headers, it at least ran through the prodigal step and almost all of the HMMsearch step (when 99% complete). Now it doesn't even make it out of the prodigal step (it finished 17,500 of the 42,000 assemblies). So any tips for what to try next would be greatly appreciated! Thanks!

Environment

uncertain - this is on a remote server

Server information

CPU: model name : Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz 40
RAM - I'm requesting 108Gb RAM on compute node
OS:
AME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

Debugging information

gtdbtk.log

pchaumeil commented 10 months ago

Hello, Did you manage to find what is happening during the Prodigal step?

youngeryu commented 9 months ago

Hello, I have encountered the same problem and it has not been resolved yet. If your problem is resolved, please display your answer on this webpage. Thank you!

agmpo commented 9 months ago

Sorry I did not find a solution for this.

youngeryu commented 9 months ago

Sorry I did not find a solution for this.

I found that the issue no longer occured when the latest version, i.e, v2.3.2, was installed, whereas I previously installed v2.1.1. I hope this can help you too.

agmpo commented 9 months ago

Thank you ... I'm already using v2.3.2 unfortunately. Glad it worked for you though and happy annotating!

pchaumeil commented 5 months ago

Ticket closed due to inactivity.

Ecogenomics / GTDBTk