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lskatz / mashtree

:deciduous_tree: Create a tree using Mash distances
GNU General Public License v3.0
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mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value #64

Closed mdiricks closed 2 years ago

mdiricks commented 3 years ago

Describe the bug I´m running mashtree v.1.2.0 on about 3500 samples, both on a VM with 30 threads and on a slurm controlled system with 10 threads. Both with ubuntu 20.04 LTS. On the VM with 30 threads, it always gets stuck in a step "joining thread" or "calcualting distances", without generating an error. On slurm, it produces all the msh files, distance and phylip file but fails in the last step to make a tree with error mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value. Any idea?

lskatz commented 3 years ago

This usually happens if at least one file is not good. Can you make sure they're all correctly fastq.gz format?

ls -lsL .fastq.gz file .fastq.gz

JosephWestley commented 2 years ago

I am also encountering the above error when trying to run mashtree on certain genomes, but then it seems to work fine on others. I am using complete assembled genomes downloaded from NCBI in .fna format.I can't seem to figure out why it works fine for some taxa and generates the above error for others. Any help you can provide would be greatly appreciated!

lskatz commented 2 years ago

I am going to close this thread as old. If you have the samples, I might be able to try to replicate the error and reopen this.