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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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hal2maf Error: PermissionError: [Errno 13] Permission denied: 'halStats' #1355

Open tinaveit opened 5 months ago

tinaveit commented 5 months ago

Hi, We are using cactus-hal2maf command but facing an error (PermissionError: [Errno 13] Permission denied: 'halStats'). Cactus version is the latest (released on 4/4/2024). Also, I was facing a Docker error previously that seems to be fixed by doing: export PATH=$PATH:/mnt/research/xtremodevo/maf_files/cactus-bin-v2.8.1/cactus-bin-v2.8.1/bin The command I am using to run is: (cactus_env) (base) -bash-4.2$ cactus-hal2maf ./jS /mnt/research/xtremodevo/maf_files/output.hal output.maf.gz --dupeMode single --refGenome Nematolebias_whitei --noAncestors --chunkSize 1000000 --binariesMode local

I have attached the log as well. Any help is appreciated. Thanks! (cactus_env) (base) -bash-4.pdf

glennhickey commented 5 months ago

This looks like an installation problem... Are you able to run halStats from the command prompt?

tinaveit commented 5 months ago

No, it says "permission denied."

glennhickey commented 5 months ago

Well, I guess the first thing is to check to make sure you installed cactus exactly folliwing the instructions https://github.com/ComparativeGenomicsToolkit/cactus/blob/v2.8.1/BIN-INSTALL.md and that you're on a x86 system.

Unfortunately, --binariesMode docker doesn't work for this tool (fixed in next release), but you can also run without installing cactus inside docker with 

docker run -it --rm -v /mnt/research/xtremodevo/maf_files/:/data quay.io/comparative-genomics-toolkit/cactus:v2.8.1 cactus-hal2maf /data/js /data/output.hal /data/output.maf.gz --dupeMode single --refGenome Nematolebias_whitei --noAncestors --chunkSize 1000000