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Placing bins in reference genome tree problem #37
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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 Cheers, |
Hello, CheckM appears to be crashing when calling Cheers, |
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 |
Given the output has the line `Killed` did pplacer run out of memory?
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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. |
Thanks, that was the problem. I've increased the RAM on my VM. Thanks so much! Elena |
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.
[CheckM - tree] Placing bins in reference genome tree.
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
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