ValueError: max() arg is an empty sequence" error

[aboffin]

Hi,

I pulled the latest version of "2.blca_main.py", running it gives the error: "ValueError: max() arg is an empty sequence"

In addition, initially, I got "ERROR: clustalo is NOT in your PATH, please set up clustalo!" Installing crustal-omega solves the issue.

The README file only specifies BLASTN and MUSCLE to be in the PATH but does not say anything about clustal-omega.

However, I get the "max() arg is an empty sequence error".

python /Users/sen/git_repos/BLCA/2.blca_main.py -i otu_ungap.fasta \
 -r /Users/sen/git_repos/BLCA/db/16SMicrobial.ACC.taxonomy \
 -q /Users/sen/git_repos/BLCA/db/16SMicrobial;

clustalo is located in your PATH!
>  > Fasta file read in!
>  > Reading in taxonomy information! ....
blastn is located in your PATH!
> > Running blast!!
> > Blastn Finished!!
>  > read in blast file...
>  > blastn file opened
>  > blast output read in
>  > Start aligning reads...
Cut offs
('evalue:', 0.1, 'identity:', 90.0, 'coverage:', 0.85)
Traceback (most recent call last):
  File "/Users/sen/git_repos/BLCA/2.blca_main.py", line 329, in <module>
    mx=max(tmpdic.values())
ValueError: max() arg is an empty sequence

[yingeddi2008]

Hi Senthil,

Thanks for the feedback. I will make appropriate changes to the README file and test on the updated package. Since we are accepting other collaborators' contribution to the main function, it needs more testing than usual to have smoothly-running software.

Thanks again for your support, I will get the software running as soon as possible.

Eddi

On Thu, Nov 15, 2018 at 12:49 PM Senthil Murugapiran < notifications@github.com> wrote:

Hi,

I pulled the latest version of "2.blca_main.py", running it gives the error: "ValueError: max() arg is an empty sequence"

In addition, initially, I got "ERROR: clustalo is NOT in your PATH, please set up clustalo!" Installing crustal-omega solves the issue.

The README file only specifies BLASTN and MUSCLE to be in the PATH but does not say anything about clustal-omega.

However, I get the "max() arg is an empty sequence error".

python /Users/sen/git_repos/BLCA/2.blca_main.py -i otu_ungap.fasta \ -r /Users/sen/git_repos/BLCA/db/16SMicrobial.ACC.taxonomy \ -q /Users/sen/git_repos/BLCA/db/16SMicrobial;

clustalo is located in your PATH!

Fasta file read in! Reading in taxonomy information! .... blastn is located in your PATH! Running blast!! Blastn Finished!! read in blast file... blastn file opened blast output read in Start aligning reads... Cut offs ('evalue:', 0.1, 'identity:', 90.0, 'coverage:', 0.85) Traceback (most recent call last): File "/Users/sen/git_repos/BLCA/2.blca_main.py", line 329, in mx=max(tmpdic.values()) ValueError: max() arg is an empty sequence

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[aboffin]

Hi Eddi,

Reverting back to an earlier commit seems to resolve the issue. Is it possible to revert back the last commit till you resolve the script and may be commit it once you are sure all tests pass? This will save headache for others who are downloading the latest (but non-working) version from GitHub.

Thanks, Senthil

python /Users/sen/git_repos/BLCA/2.blca_main_aboffin.py \
 -i otu_ungap.fasta \
 -r /Users/sen/git_repos/BLCA/db/16SMicrobial.ACC.taxonomy \
 -q /Users/sen/git_repos/BLCA/db/16SMicrobial;
blastdbcmd is located in your PATH!
muscle is located in your PATH!
>  > Fasta file read in!!
>  > Reading in taxonomy information! ....
blastn is located in your PATH!
> > Running blast!!
> > Blastn Finished!!
>  > Read in blast output!
>> Taxonomy file generated!!

[yingeddi2008]

Hi Senthil,

I prepared a release of the previous version of the software at https://github.com/qunfengdong/BLCA/releases. It is the python2.7 compatible one. I will update the README file accordingly. You can download the source code, unzipp it. And it should be identical to the package before the python 3 version.

Let me know if you have any further questions,

Thanks,

Eddi

On Thu, Nov 15, 2018 at 2:40 PM Senthil Murugapiran < notifications@github.com> wrote:

Hi Eddi,

Reverting back to an earlier commit seems to resolve the issue. Is it possible to revert back the last commit till you resolve the script and may be commit it once you are sure all tests pass? This will save headache for others who are downloading the latest (but non-working) version from GitHub.

Thanks, Senthil

python /Users/sen/git_repos/BLCA/2.blca_main_aboffin.py -i otu_ungap.fasta -r /Users/sen/git_repos/BLCA/db/16SMicrobial.ACC.taxonomy -q /Users/sen/git_repos/BLCA/db/16SMicrobial blastdbcmd is located in your PATH! muscle is located in your PATH!

Fasta file read in!! Reading in taxonomy information! .... blastn is located in your PATH! Running blast!! Blastn Finished!! Read in blast output! Taxonomy file generated!!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/13#issuecomment-439182342, or mute the thread https://github.com/notifications/unsubscribe-auth/AHCP00KxLQeCDplpGV_6PWw0gAkKqNlTks5uvdElgaJpZM4YhoEa .

[aboffin]

Thanks Eddi!

[ChouhanDheeraj]

Hi,

I pulled the latest version of "2.blca_main.py", running it gives the error: "ValueError: max() arg is an empty sequence"

In addition, initially, I got "ERROR: clustalo is NOT in your PATH, please set up clustalo!" Installing crustal-omega solves the issue.

The README file only specifies BLASTN and MUSCLE to be in the PATH but does not say anything about clustal-omega.

However, I get the "max() arg is an empty sequence error".

python /Users/sen/git_repos/BLCA/2.blca_main.py -i otu_ungap.fasta \
 -r /Users/sen/git_repos/BLCA/db/16SMicrobial.ACC.taxonomy \
 -q /Users/sen/git_repos/BLCA/db/16SMicrobial;

clustalo is located in your PATH!
>  > Fasta file read in!
>  > Reading in taxonomy information! ....
blastn is located in your PATH!
> > Running blast!!
> > Blastn Finished!!
>  > read in blast file...
>  > blastn file opened
>  > blast output read in
>  > Start aligning reads...
Cut offs
('evalue:', 0.1, 'identity:', 90.0, 'coverage:', 0.85)
Traceback (most recent call last):
  File "/Users/sen/git_repos/BLCA/2.blca_main.py", line 329, in <module>
    mx=max(tmpdic.values())
ValueError: max() arg is an empty sequence

Hello @aboffin I am getting same error of 'clustalo is NOT in your PATH, please set up clustalo!' How can I resolve this ? Can you please help me in this?

[qunfengdong]

Hello @ChouhanDheeraj, thank you for using BLCA. Could you try to install clustalo and add it to your PATH? Please let us know if you still have trouble doing that, thanks.