Closed ceya closed 7 years ago
Hello Brooke,
CompareM is still in active development, but I am very surprised to hear this result. Do you mind sending my your genome files and the exact command you are running so I can investigate?
Cheers, Donovan (donovan.parks [at] gmail.com)
Hello Donovan,
Of course, attached are two of my faa files. I used default setting comparem aai_wf test aai_output (test being my directory containing the faa files). I also tried adjusting the e-value and identity cutoff but it didn't help much. I'd really appreciate if you could have a look and help me identify what might be the issue.
Thank you very much! Brooke
On Tue, Jul 5, 2016 at 2:46 PM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
CompareM is still in active development, but I am very surprised to hear this result. Do you mind sending my your genome files and the exact command you are running so I can investigate?
Cheers, Donovan (donovan.parks [at] gmail.com)
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Hello Brooke,
I don't see any attached files. Any chance you forgot to attach them? :)
Cheers, Donovan
Hi Donovan,
Can you see them now? I attached four faa files this time.
Regards, Brooke
On Mon, Jul 11, 2016 at 4:32 PM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
I don't see any attached files. Any chance you forgot to attach them? :)
Cheers, Donovan
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Hello Brooke,
GitHub is very strict on what files can be attached. Can you just email them to me directly at donovan.parks [at] gmail.com.
Thanks, Donovan
Done!
On Tue, Jul 12, 2016 at 9:46 AM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
GitHub is very strict on what files can be attached. Can you just email them to me directly at donovan.parks [at] gmail.com.
Thanks, Donovan
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Hello Brooke,
CompareM processes your genomes fine on my end. I am running the program as follows:
comparem aai_wf test aai_output --file_ext faa --proteins --cpus 40
The file_ext
flag indicates that *.faa files should be processed and the proteins
flag indicates the FASTA files already contain proteins so gene calling is not necessary. The results indicate that all these genomes are nearly identical (AAI >= 99.98%).
Can you verify that you have the latest version of CompareM (v0.0.16) and DIAMOND >= v0.8.10?
Cheers, Donovan
Hi Donovan,
I've compareM 0.0.16 and diamond v0.8.10.72. I ran the same command except for the --cpu setting and still have 0 orthologs.
Could it be that the program wasn't installed correctly? I send the whole aai_output folder to your gmail account. Could you take a look at the files?
Thank you very much! Brooke
On Tue, Jul 12, 2016 at 11:37 AM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
CompareM processes your genomes fine on my end. I am running the program as follows: comparem aai_wf test aai_output --file_ext faa --proteins --cpus 40
The file_ext flag indicates that *.faa files should be processed and the proteins flag indicates the FASTA files already contain proteins so gene calling is not necessary. The results indicate that all these genomes are nearly identical (AAI >= 99.98%).
Can you verify that you have the latest version of CompareM (v0.0.16) and DIAMOND >= v0.8.10?
Cheers, Donovan
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Hello Brooke,
I think it may have to do with different flavours of Linux. What OS are you using?
Cheers, Donovan
Can you also try running CompareM on just the 4 genome you sent me and then sending me the output directory for this? This way I can directly compare my output to your to see where they differ.
I'm using a terminal with 64-bit Linux CentOS
On Tue, Jul 12, 2016 at 1:01 PM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
I think it may have to do with different flavours of Linux. What OS are you using?
Cheers, Donovan
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Hello Brooke,
Thank you for helping with the debugging. It does appear to be a Linux flavour issue. Specifically, it has to do with the sort
command of the OS. CompareM uses sort to index the resulting DIAMOND hits file and I can see that on your machine the file is not actually sorted. Can you check which sort you have on your path (i.e., run which sort
and let me know what it returns). I'm digging around the net to see if this is a CentOS issue, but I suspect you may just have a different sort
program on your path other than the standard Unix program.
Thanks Donovan
Hi Donovan,
Here's the output: [brooke@tatanka comparem]$ which sort /bin/sort
On Tue, Jul 12, 2016 at 1:31 PM, Donovan Parks notifications@github.com wrote:
Hello Brooke,
Thank you for helping with the debugging. It does appear to be a Linux flavour issue. Specifically, it has to do with the sort command of the OS. CompareM uses sort to index the resulting DIAMOND hits file and I can see that on your machine the file is not actually sorted. Can you check which sort you have on your path (i.e., run which sort and let me know what it returns). I'm digging around the net to see if this is a CentOS issue, but I suspect you may just have a different sort program on your path other than the standard Unix program.
Thanks Donovan
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Hey,
Seem like this may be a bug with the CentOS implementation of sort: https://bugs.centos.org/view.php?id=9289
Perhaps you need to update to coreutils-8.22-13.el7.
Cheers, Donovan
Thanks Donovan! I'll contact the admins and let them know.
Regards, Brooke
On Tue, Jul 12, 2016 at 1:43 PM, Donovan Parks notifications@github.com wrote:
Hey,
Seem like this may be a bug with the CentOS implementation of sort: https://bugs.centos.org/view.php?id=9289
Perhaps you need to update to coreutils-8.22-13.el7.
Cheers, Donovan
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Hello Same results here (no Orthologs found) in OSX 10.11.6 every required binaries were installed or compiled(Diamond)
which sort sort is /usr/bin/sort
Incase this is useful for future strugglers, installing comparem into a conda env with bioconda coreutils overcame this issue for me.
conda create -n comparem python=2.7 scipy
conda install --name comparem -c bioconda coreutils
source activate comparem
pip install comparem
Hello,
I'm using the default setting of comparem aai_wf to calculate aai between my faa genome files and the program cannot find any orthologs. but with the AAI calculator by Kostas lab the score is 99. Does anyone know what might be the problem?
Thank you! Brooke