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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
43 stars 14 forks source link

Issues about bowtie2 #45

Closed jeniferclopes closed 4 years ago

jeniferclopes commented 4 years ago

I am trying to run FastPlast but I got stuck here:

Can't exec "/home/geninfo/jdantas/Fast-Plast/bin/bowtie2-2.3.5.1/bowtie2-build": No such file or directory at fast-plast.pl line 1169. Can't exec "/home/geninfo/jdantas/Fast-Plast/bin/bowtie2-2.3.5.1/bowtie2": No such file or directory at fast-plast.pl line 593. No mapped reads files were identified to run SPAdes. Please check 2_Bowtie_Mapping.

How can I fix these issues? I followed the installation walkthrough.

Thanks

mrmckain commented 4 years ago

This suggests that you don't have bowtie installed where Fast-Plast is checking. Is this the correct path: /home/geninfo/jdantas/Fast-Plast/bin/bowtie2-2.3.5.1/bowtie2-build? If so, do you have access to it?

jeniferclopes commented 4 years ago

Thanks for your reply! We have solved the problem. The INSTALL.pl script named the folder where Bowtie was installed with a different name used by the fast-plast.pl script to call Bowtie. The problem was in the PATH.

Best Regards, Jenifer

Jenifer de Carvalho Lopes

Em qui., 9 de abr. de 2020 às 14:18, Michael McKain < notifications@github.com> escreveu:

This suggests that you don't have bowtie installed where Fast-Plast is checking. Is this the correct path: /home/geninfo/jdantas/Fast-Plast/bin/bowtie2-2.3.5.1/bowtie2-build? If so, do you have access to it?

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mrmckain commented 4 years ago

Great to hear.