Shorah throwing error for PacBio bam files

[zusman]

Hi, I have already used shorah for Illumina analysis, But for Pacbio bam file it is throwing this Error:

$ ~/Apps/shorah/shorah.py -b ~/Desktop/noro/file.2-2.consensusreadset_aligned.bam -f ~/Desktop/noro/EU078417_NG12372.fasta /home/Apps/shorah/diri_sampler/home/Apps/shorah/diri_sampler: : error while loading shared librarieserror while loading shared libraries: : libgsl.so.0libgsl.so.0: : cannot open shared object filecannot open shared object file: : No such file or directoryNo such file or directory

Can you please help me, what possibly be going wrong?? Best Zusman

[ozagordi]

Hi @zusman, and my apologies for replying so late. Did you solve this issue? It doesn't seem related to Pacbio, but rather to your system. I would suggest searching the web for "error while loading shared libraries" first.

[zusman]

Dear Zargordi,

I dint seem to fix the issue. I had to provide the results urgently so I used other means. But I would like to know if Shorah works fine for pacbio reads. Can you suggest what input parameters are required by shorah when running PacBio platform ccs reads??

Best Zainab

On 20. Feb 2018, at 1:46 PM, Osvaldo Zagordi notifications@github.com wrote:

Hi @zusman https://github.com/zusman, and my apologies for replying so late. Did you solve this issue? It doesn't seem related to Pacbio, but rather to your system. I would suggest searching the web for "error while loading shared libraries" first.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cbg-ethz/shorah/issues/39#issuecomment-366966727, or mute the thread https://github.com/notifications/unsubscribe-auth/APfdnbyShPPnj6FdlE7I_eO8b_Wlmfrhks5tWr68gaJpZM4RAb53.

[ozagordi]

I don't have a direct experience with Pacbio reads, so I'm not sure I can say anything really useful. Usual suggestions would apply:

• check whether you are in shotgun mode or amplicon mode (see docs);
• use a window length slightly shorter than typical read length;
• ask yourself if global reconstruction is really needed, use other tools if this is the case.

I'm closing this now.