Failed SalmonTE example run

hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

GNU General Public License v3.0

81 stars 23 forks source link

Failed SalmonTE example run #19

Closed wesleylcai closed 5 years ago

wesleylcai commented 5 years ago

I followed the example code and ran SalmonTE.py quant --reference=hs ~/programs/SalmonTE/example/

However, I got this error: KeyError in line 3 of /home/wc376/programs/SalmonTE/snakemake/Snakefile.paired: 'index' File "/home/wc376/programs/SalmonTE/snakemake/Snakefile.paired", line 3, in <module> Will exit after finishing currently running jobs. 2018-08-26 18:23:14,773 Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

Any ideas? I am running with Python 3.5.1, snakemake-5.2.2, pandas-0.23.4, docopt-0.6.2

hyunhwan-jeong commented 5 years ago

Hello @wescaiju,

I can't generate the same message using the command-line. One thing I am suspecting is the version of snakemake is 5.2.2, and SalmonTE is not guaranteed to run with the latest version of snakemake. Can you downgrade snakemake to 5.1.5 and rerun it again? Please refer this link if you don't know how to downgrade the version of snakemake. https://github.com/hyunhwaj/SalmonTE/issues/14#issuecomment-408705766

Best Regards,

Hyun-Hwan Jeong

hyunhwan-jeong commented 5 years ago

I close this issue because it is been a while since I have asked, but no response.