UCSBMicrobiologyCore
commented
8 years ago I apparently missed some of the output for the first issue. Here's what I got when I reran:
[CheckM - tree] Placing bins in reference genome tree.
Identifying marker genes in 115 bins with 1 threads: [Error] Input file does not exists: /home/tarn/archaeatree/bins/Aciduliprofundum boonei T469/genes.gff.4
Saving HMM info to file.
Calculating genome statistics for 115 bins with 1 threads: Finished processing 115 of 115 (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 1 threads: Finished extracting 43 of 43 (100.00%) HMMs. Aligning 43 marker genes with 1 threads: Finished aligning 43 of 43 (100.00%) marker genes.
Reading marker alignment files. Concatenating alignments. Placing 115 bins into the genome tree with pplacer (be patient).
{ Current stage: 0:04:45.100 || Total: 0:04:45.100 }
it is telling me that something does not exist for my file '/home/tarn/archaeatree/bins/Aciduliprofundum boonei.fasta'. And then checkm assumedly just stops trying to look for marker genes in the rest of the bins, which explains the output issues I was having, but not why it does this.
Is there some other information I need that I have not provided? The file format I inputed for this specific bin was simply the entire genome pasted into a fasta file. According to the bin stats tree tsv checkm can read and understand this format, so I'm not sure what the issue might be.
Jon
donovan-h-parks
Hi Dr Parks;
I'm having two separate issues:
-firstly, I did a run of checkm tree as follows: checkm tree --ali --nt -x fasta /home/tarn/archaeabins /home/tarn/archaeatree
with a folder containing a whole bunch of different ncbi genomes and four of my bins which I wanted to determine the taxonomy of. When I did this, the entire thing ran to completion, but when I look at the output, it's clear that it read the first bin and did not complete the rest. That's my first issue.
I'm hoping that was a memory issue (as I type this I'm going to try reduced tree to see if it helps). That said, there was a tree file created listed as concatenated.tre. I assumed that was the output tree but when I opened it in a tree-editing program, it shows a small tree of 5 IMG genomes. I tried running the tree command with a few other subsets of genomes and I got the same tree as a reult, and those also proceeded to completion, i.e.:
Identifying marker genes in 4 bins with 1 threads: Finished processing 4 of 4 (100.00%) bins. Saving HMM info to file.
Calculating genome statistics for 4 bins with 1 threads: Finished processing 4 of 4 (100.00%) bins.
Extracting marker genes to align. Parsing HMM hits to marker genes: Finished parsing hits for 4 of 4 (100.00%) bins. Extracting 43 HMMs with 1 threads: Finished extracting 43 of 43 (100.00%) HMMs. Aligning 43 marker genes with 1 threads: Finished aligning 43 of 43 (100.00%) marker genes.
Reading marker alignment files. Concatenating alignments. Placing 4 bins into the genome tree with pplacer (be patient).
...my second issue is--what is this tree and why was it made with these specific genomes?
thank you
Jon