GTDBTk
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Ecogenomics
gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.
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
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CPU: model name : Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz 40
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RAM - I'm requesting 108Gb RAM on compute node
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OS:
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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
Hello, Did you manage to find what is happening during the Prodigal step?
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!
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.
Thank you ... I'm already using v2.3.2 unfortunately. Glad it worked for you though and happy annotating!