Error in vars()

[homopolymer]

I ran snv.py in my data, but got the following error information. How to resolve it?

Traceback (most recent call last): File "/tool/shorah/snv.py", line 440, in main(_args, *_vars(opts)) TypeError: vars() argument must have dict attribute

[ozagordi]

Hi. Could you please try again with the version I just pushed? Please note the steps you are taking (input, the commands you give and the output) and let me know.

[homopolymer]

Hi Ozagordi

Thanks for the quick reply. I tried the new script, this issue has been solved. However, another issue comes out.

Here is the command that I tried, $ python ~/tool/shorah/snv.py -r hiv_hxb2.fasta -b hiv_pacbio.bwa-mem.bam

But I got the error information: "Coverage file generated by b2w not found." Is there anything I miss here?

[ozagordi]

Did you recompile?

On 27 August 2014 13:33, homopolymer notifications@github.com wrote:

Hi Ozagordi

Thanks for the quick reply. I tried the new script, this issue has been solved. However, another issue comes out.

Here is the command that I tried, $ python ~/tool/shorah/snv.py -r hiv_hxb2.fasta -b hiv_pacbio.bwa-mem.bam

But I got the error information: "Coverage file generated by b2w not found." Is there anything I miss here?

— Reply to this email directly or view it on GitHub https://github.com/ozagordi/shorah/issues/7#issuecomment-53557117.

Ciao. Osvaldo

[homopolymer]

Yes, I re-git clone the repo and make.

[ozagordi]

Are you running in local mode or global mode (see http://ozagordi.github.io/shorah/)? The first is launched with dec.py (shotgun) or amplian.py (amplicon). The second with shorah.py. If you are interested in global reconstruction, you should know that there are more recent softwares. Make sure that you have enough coverage. Given that you are passing the whole HIV genome as reference, did you make sure you have coverage everywhere? Since you are not giving to me the full background of your analysis, it's hard for me to guess.

On 27 August 2014 15:58, homopolymer notifications@github.com wrote:

Yes, I re-git clone the repo and make.

— Reply to this email directly or view it on GitHub https://github.com/ozagordi/shorah/issues/7#issuecomment-53575902.

Ciao. Osvaldo

[homopolymer]

I am looking for a tool to call SNV in hiv sequencing data. I previously thought snv.py as a standalone script in the shorah package for snv calling. So I ran snv.py solely, and tried to use it to call snv. I think I misunderstood here. I also tried dec.py and shorah.py after recompile. Both of them work well right now. Thanks a lot.

[ozagordi]

snv.py is called by dec.py and amplian.py. Unless you are in a special case you shouldn't call it yourself. I would like to know your experience with the SNVs called at the end. I will close this issue.

On 28 August 2014 09:41, homopolymer notifications@github.com wrote:

I am looking for a tool to call SNV in hiv sequencing data. I previously thought snv.py as a standalone script in the shorah package for snv calling. I think I misunderstood here. I also tried dec.py and shorah.py after recompile. Both of them work well right now. Thanks a lot.

— Reply to this email directly or view it on GitHub https://github.com/ozagordi/shorah/issues/7#issuecomment-53683414.

Ciao. Osvaldo

[ibseq]

Hi Osvaldo, catching up with issue above, with my command : shorah snv -b test_sorted.bam -f ~/ref/MN908947.3.fasta -of vcf

I'm getting Coverage file generated by b2w not found.

Any advice? Also, how can we run shorah on multiple bam files simultaneously ? I have tried vpipe as well but for some reason the vcf file was empty!

thanks! ibseq