No pairwise aai statistics come out.

[minsookim1983]

Hello,

I did aai_wf workflow of comparem with default settings to calculate aai between assembled contigs, and no orthologs come out in output dir. I checked all the steps, and I found that there was something wrong in similarity step. Specifically, the file named "hits_sorted.tsv" is empty.

What I put it in first in console, $ comparem aai_wf input_dir/ aai_output/ -x fa --blastp -c 10 ; but I did not get anything and no data was observed in "hits_sorted.tsv".

Next I did similarity only, $ comparem similarity aai_output/genes/ aai_output/genes/ similarity_output/ -x faa --blastp -c 10 ; but I did not get anything either. So, I tried it again with the values of --per_identity (-p 0) and --per_aln_len (-a 0), but I did not get anything.

No error messages were shown when doing comparem. I tested it again with NCBI bacterial genomes; it does not work either.

My system is Ubuntu 14.04 x64. Typing with "which sort", I got "/usr/bin/sort". Do you know what might be the problem?

Thank you for your help! Min-Soo

[donovan-h-parks]

Hello Min-Soo,

Did you resolve this issue?

Cheers, Donovan

[minsookim1983]

Thank you for your answer. Not yet. I have no idea of how to resolve this issue.

Min-Soo

On 3 Jan 2017, at 4:13 AM, Donovan Parks notifications@github.com wrote:

Hello Min-Soo,

Did you resolve this issue?

Cheers, Donovan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[minsookim1983]

Does it look like that there is a problem in my system? Do my output files support you to figure out what the problem is? I am looking for aai calculator. My data is large and numerous, so I think your CompareM is the only tool for me. I will wait for your response.

Thank you for your kind. Min-Soo

On Tue, Jan 3, 2017 at 8:05 AM, Min-Soo Kim cannavarosoo@gmail.com wrote:

Thank you for your answer. Not yet. I have no idea of how to solve this issue.

Min-Soo

On 3 Jan 2017, at 4:13 AM, Donovan Parks notifications@github.com wrote:

Hello Min-Soo,

Did you resolve this issue?

Cheers, Donovan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dparks1134/CompareM/issues/9#issuecomment-270010006, or mute the thread https://github.com/notifications/unsubscribe-auth/AT2AilofzjiJjJsWLuhylduzV8EYyCWbks5rOUw9gaJpZM4LU1nY .

[donovan-h-parks]

Hello Min-Soo,

Can you make sure you have the latest version of both CompareM (v0.0.21) and biolib (v0.0.34) on your system? If the problem still persists, can you narrow the issue down to a pair on input files and send these to me at donovan.parks [at] gmail.com along with the exact command you ran so I can debug the issue.

Regards, Donovan

[minsookim1983]

Thank you for your answer. I check the version of both CompareM and biolib on my system, and I found that 'sudo pip install' and the version of biolib (v0.0.34) were in trouble. Now, I confirmed that it works well. I appreciate your consideration.

Min-Soo

On Sat, Jan 7, 2017 at 1:16 AM, Donovan Parks notifications@github.com wrote:

Hello Min-Soo,

Can you make sure you have the latest version of both CompareM (v0.0.21) and biolib (v0.0.34) on your system? If the problem still persists, can you narrow the issue down to a pair on input files and send these to me at donovan.parks [at] gmail.com along with the exact command you ran so I can debug the issue.

Regards, Donovan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dparks1134/CompareM/issues/9#issuecomment-270939260, or mute the thread https://github.com/notifications/unsubscribe-auth/AT2AigHty4Ft6lb5wZwq0LwbrSSUOgoDks5rPmj6gaJpZM4LU1nY .

[donovan-h-parks]

Excellent. Glad to hear it.