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cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
GNU General Public License v3.0
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install mac #34

Closed antoine4ucsd closed 7 years ago

antoine4ucsd commented 7 years ago

Hi, I am very interested in your software to use on MiSeq HIV data I've just installed haploclique on my Mac with the followings: git clone https://github.com/cbg-ethz/haploclique && cd haploclique git submodule update --init --remote mkdir build && cd build cmake .. && make No errors. Haploclique should now be installed in the following dir: /Users/myname/Documents/haploclique/

When I tried to test it on bam file with the following command but I get this error:

screen shot 2017-03-15 at 10 07 12 am

It is probably something obvious...Any chance you can help me? Let me know if you need any other info. thanks! a

armintoepfer commented 7 years ago
antoine4ucsd commented 7 years ago

thanks Armin! Just realized that haploclique-assembly was deprecated. I tried the following command on some sample test and I got the following:

screen shot 2017-03-15 at 10 39 59 am

I will keep working on it but if you see any obvious mistake, all advices are warmly welcome! thanks again,

armintoepfer commented 7 years ago

Looks like the libbamtools library is not in your LD_LIBRARY_PATH. It should be have been compiled along the binary. If you find it, add the absolute path like

export DYLD_LIBRARY_PATH=/your/path/to/the/lib/dir:$DYLD_LIBRARY_PATH

Let us know how it went

antoine4ucsd commented 7 years ago

Yeah! For some reason, I had to export the libbamtools library as you suggested even if it was installed in my path: usr/local/lib/bamtools Anyway, I am running a first test on interleaved paired end MiSeq HIV reads already cleaned and filtered with our local pipeline. I would be very interested in sharing with you our first results. I will play around all the option. It doesn't look like the -r (for reference) is in the arg list anymore though?

thanks again for being so responsive! a

armintoepfer commented 7 years ago

My pleasure. The internals have been enhanced, thus the re-alignment step and the necessity of a reference has been obsoleted.

antoine4ucsd commented 7 years ago

thanks! We are currently using both PacBio and MiSeq platform in the lab. For the latter (reads ~250-350bp), I was willing to map and reassemble long amplicons from filtered cleaned reads encompassing a given region based on primers from the attached paper. Do you think this is unrealistic?

The basic command I just used generated hundreds of short ‘clique’ variants. haploclique F1map.bam F1.out

the data input are my interleaved reads after clean up and filtering using the following pipeline: https://github.com/iosonofabio/hivwholeseq https://github.com/iosonofabio/hivwholeseq

If you are interested and if you have time(…), I would be happy to have your thoughts about it

thanks, a

On Mar 15, 2017, at 11:11 AM, Armin Töpfer notifications@github.com wrote:

My pleasure. The internals have been enhanced, thus the re-alignment step and the necessity of a reference has been obsoleted.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/cbg-ethz/haploclique/issues/34#issuecomment-286831588, or mute the thread https://github.com/notifications/unsubscribe-auth/ARpT501L_5afrefu5lPAYqZu6da8ZGR3ks5rmCnZgaJpZM4MeQFk.

tobiasmarschall commented 7 years ago

@armintoepfer @MaryamZaheri We should provide a bioconda recipe to easy installation. I will create an issue for this.

@antoine4ucsd We will have a tutorial on virus sequencing that will also cover haploclique at BC2 on Sept 12. Maybe that'd be a good opportunity to get in touch in person. (In the meantime, we are of course happy to discuss online.)

antoine4ucsd commented 7 years ago

Thank you both! @tobiasmarschall , I'd love to assist this conference but not sure if I'll be able to make it. While my install seems to have worked properly, I am struggling with the first generated variants. I guess smthg went wrong. We can share a set of data if you have time to take a quick look. I was able to generate realistic allele freq and a pretty good coverage with my own pipeline and the consensi are fine (generated with my pipeline or with IVA). My goal would be to reconstruct some 'representative' haplotypes from these long amplicons. Any advices? Specific options on haplocliques? The bam file I used as input for haploclique is the cleaned filtered interleaved reads obtained with my pipeline. We can close this post and discussed about it online. Thanks again!

tobiasmarschall commented 7 years ago

@MaryamZaheri Would you have time to look at such a data set? I think it would be valuable to figure out what might have gone wrong.

MaryamZaheri commented 7 years ago

Hi all,

I would be more than happy help. @antoine4ucsd If it is possible please share your data so I can take a look. How large is you data file?

antoine4ucsd commented 7 years ago

I can send you a subset of reads. How should we proceed?

thanks!

MaryamZaheri commented 7 years ago

If it is less than 10Mb send it by email to maryam.zaheri@bsse.ethz.ch. Otherwise share it with google drive or ftp, my account is zaheri@gmail.com.