Comments (7)
from checkm.
Good call Ben. Elena, how much memory (RAM) does your machine have? If you have <32GB, you should pass the --reduced_tree flag which works on machines with 16GB.
from checkm.
Hello,
I haven't run across this issue before. Can you send me the exact command you are running? Also, can you verify that the file ./testOUT/storage/tree/concatenated.pplacer.json
exists.
Cheers,
Donovan
from checkm.
Hi Donovan,
I ran the command
~ $ checkm tree ~/checkm/test_data/ ~/Desktop/tree_testOUT/
(same result with checkm lineage_wf -t 4 ~/checkm/test_data/ ~/Desktop/tree_testOUT/)
tree_testOUT/storage/tree/concatenated.pplacer.json does not exist (tree_testOUT/storage/tree directory contents below)
However, running
~ $ checkm test ~/Desktop/checkm_testOUT
seems to have worked, and the concatenated.pplacer.json file does exist
Cheers,
Elena
from checkm.
Hello,
CheckM appears to be crashing when calling pplacer
. Can you verify that you are using the latest version of pplacer (v2.6.32; also called v1.1.alpha16). Alternatively, it may be a subtle issue with your genome that I have not encountered. I'd be happy to look into it if you want to send me your genome.
Cheers,
Donovan
from checkm.
Hello,
I am running pplacer-v1.1.alpha16. I also wondered whether there was an issue with my genomic data, so I used the E. coli genome provided in the test_data directory (/checkm/test_data/637000110.fna) to test checkm tree and checkm lineage_wf. The above results are using 637000110.fna.
Thanks for your help.
Elena
from checkm.
Thanks, that was the problem. I've increased the RAM on my VM. Thanks so much!
Elena
from checkm.
Related Issues (20)
- FileNotFoundError for concatenated.tre file? HOT 1
- Unexpected error: <class 'RecursionError'> HOT 2
- Placing 3 bins into the genome tree with pplacer Killed HOT 4
- AttributeError: 'Namespace' when running 'checkm coverage' HOT 1
- bin_qa_plot
- Customizing CheckM Dataset & Gene Marker Selection for a Species
- Reference data is missing HOT 1
- don't find Strain heterogeneity info
- FileNotFoundError: [Errno 2] No such file or directory: 'checkm_folder/storage/tree/concatenated.tre' HOT 8
- IndexError: list index out of range HOT 1
- Understanding contamination value HOT 2
- ERROR conda.core.link:_execute(952): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'. HOT 1
- Unexpected error: <class 'KeyError'>
- FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' HOT 3
- Chekm test: line 1: 16491 Bus error (core dumped) pplacer -j 1 HOT 2
- maximum number of genomes/MAGs to run checkm HOT 2
- WARNING: Expected all files to contain sequences in amino acid space. HOT 1
- local variable 'seqId' referenced before assignment
- 'utf-8' codec can't decode byte 0xb0 in position 37: invalid start byte HOT 1
- checkm ssu_finder HOT 2
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from checkm.