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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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cactus-hal2maf Error #281

Open shuifeng1988 opened 1 year ago

shuifeng1988 commented 1 year ago

I tried to use cactus-hal2maf to convert hal to maf, but it can't work and I don't know the reasons!

my command has 3 steps:

  1. $docker run -p 9001:22 --name hal2maf -v /gpfs/home/mays/241mammals:/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7 /bin/bash 2.mkdir tmp
  2. cactus-hal2maf --maxDisk=10T --workDir=/data/tmp --maxMemory=350G --batchMemory=350G ./js ./241-mammalian-2020v2.hal Fruitbati.KB031032.1.maf.gz --refGenome Pteropus_alecto --refSequence KB031032.1 --chunkSize 1000000 --noAncestors

The logs: stdout.txt

glennhickey commented 1 year ago

It looks like /data/tmp and/or /data/js are somehow getting deleted while cactus is running.

shuifeng1988 commented 1 year ago

The directories are not getting deleted, they are still there after the program is killed.