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ChrisMaherLab / INTEGRATE-Vis

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Word count less than 8 Bad line 1 of fa index? #4

Open ahdee opened 6 years ago

ahdee commented 6 years ago

Hi I'm trying to run the first example. The install seem to have gone well, however, when I run it I get this error here. 

[Structure] Running Integrate-vis structure on TCGA-ZG-A8QZ-01 ...
[Structure] Making annotation file...
Word count less than 8  Bad line 1 of /scratch/index/GRCh38_r85.all.fa:

I've tried downloading different versions of the index as well as follow the github readme. However I'm stuck on this. thanks.

teng-gao commented 6 years ago

This error occurs at the step of converting the gtf to genepred. I think you mostly likely passed in a fasta file (/scratch/index/GRCh38_r85.all.fa) where you are supposed to pass in a gtf. I could re-create your error by passing a fasta as input to UCSC's gtfToGenePred. So maybe double check the usage and your parameter passing. Let me know if this works