Placing bins in reference genome tree problem

[ezaikova]

Hi,

I am having issues with "checkm tree". I installed checkm earlier this week and the "test" ran just fine. However, when I tried to analyze my bins, I got the error below. I tried running the "tree" command on the test data (which worked for "test") and still got the same error.

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[CheckM - tree] Placing bins in reference genome tree.

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Identifying marker genes in 1 bins with 4 threads:
Finished processing 1 of 1 (100.00%) bins.
Saving HMM info to file.

Calculating genome statistics for 1 bins with 4 threads:
Finished processing 1 of 1 (100.00%) bins.

Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
Extracting 43 HMMs with 4 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 4 threads:
Finished aligning 43 of 43 (100.00%) marker genes.

Reading marker alignment files.
Concatenating alignments.
Placing 1 bins into the genome tree with pplacer (be patient).
Killed
Uncaught exception: Sys_error("./testOUT/storage/tree/concatenated.pplacer.json: No such file or directory")
Fatal error: exception Sys_error("./testOUT/storage/tree/concatenated.pplacer.json: No such file or directory")

{ Current stage: 0:21:44.524 || Total: 0:21:44.524 }

I tried updating the CheckM dependency data with "sudo checkm data update", which didn't help, so then I downloaded the CheckM data (v1.0.3) and used "sudo checkm data setRoot" to point to the new directory. I still got the same error.

I am not sure if the issue is in my installation or if something is missing.

Best,

Elena

[donovan-h-parks]

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

[ezaikova]

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/)

and got the error below

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

[donovan-h-parks]

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

[ezaikova]

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

[wwood]

Given the output has the line `Killed` did pplacer run out of memory?

[donovan-h-parks]

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.

[ezaikova]

Thanks, that was the problem. I've increased the RAM on my VM. Thanks so much!

Elena