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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Failing SPAdes #41

Closed nsmt89 closed 4 years ago

nsmt89 commented 4 years ago

Hi, I saw two similar issues on failing SPAdes while using Fast-Plast but did not seem to find a solution. I used fq files as input and I checked SPAdes according to its manual and it is just fine. Could you guide me to troubleshoot? Thank you CN_1.log CN_1_Fast-Plast_Progress.log CN_1_results_out.log

I tried

  1. edit full path for dependencies in fast-plast.pl
  2. re-install
  3. choose fast-plast to install all the dependencies (except for SPAdes because they have change the repository address, so I did manually) still produce the same error.
mrmckain commented 4 years ago

The error is in where Fast-Plast is looking for the bin. Check that FPBIN is set properly (towards the beginning of the fast-plast.pl script). This should be something the Fast-Plast install does by checking where you are installing FP. Fast-Plast is unable to pull your Alismatales references from the GenBank plastomes because it cannot find the file. Best, Michael

nsmt89 commented 4 years ago

Hi,

Thanks for your help. I managed to run Fast-Plast successfully. I have another inquiries on different topic though, maybe I need to open new thread.

mrmckain commented 4 years ago

Great to hear.