Cactus 2.7.2 2024-02-23

2024/03/11 NOTE: this version does not work on AWS clusters -- use the previous or next release if specifying --batchSystem mesos --provisioner aws

Cactus 2.7.2 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.7.2
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.7.2-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.7.2.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.7.2.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.7.2.tar.gz
  Install instructions in README.md

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

The Docker images and binaries linked above are built using AVX2 extensions, and require a CPU that supports them, except the "Pre-compiled Binaries For Older CPU Architectures" which should be compatible with any 64-bit architecture (and, since version 2.3.1, support Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release Notes

This release improves MAF output, along with some other fixes

• --maxMemory option given more teeth. It is now used to clamp most large Toil jobs. On single-machine it defaults to system memory. This should prevent errors where Toil requrests more memory than available, halting the pipeline in an un-resumable state.
• Update to latest taffy and use newer MAF normalization. This should result in larger blocks and fewer gaps. MAF rows will now be sorted phylogenetically rather than alphabetically
• Better handle . characters in genome names during MAF processing. Previously neither duplicate filtering nor bigmaf summary creation could handle dots, but that should be fixed now.
• Duplicate filtering now done automatically in cactus-maf2bigmaf.
• Disable support for multifurcations (aka polytomies or internal nodes with more than 2 children) in Progressive Cactus. I'm doing this because I got spooked by a drop in coverage I noticed recently in a 4-child alignment. This regression appears to be linked to the new PAF chaining logic that's been added over the past several months. Until that's resolved, Cactus will exit with an error if it sees degree > 2 in the tree. This behaviour can, however, be overridden in the XML configuration file.