issue with running fetch

[iichelhadi]

Hi wyang17, I am having an issue with running the fetch command as shown below.

Traceback (most recent call last): File "/home/svu/phaei/.conda/miniconda/4.9/envs/squire/bin/squire", line 11, in <module> load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/hpctmp/phaei/FACT/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/hpctmp/phaei/FACT/SQuIRE/squire/Fetch.py", line 231, in main raise Exception("Was not able to download chromosome file from UCSC" + "\n", file = sys.stderr) TypeError: exceptions.Exception does not take keyword arguments

I am not sure how to resolve this issue.

regards

[ryanmboileau]

Hi, I am having the same issue-- any chance you have found a solution @iichelhadi ?

Thanks for your consideration, Ryan

[iichelhadi]

Hi, I am having the same issue-- any chance you have found a solution @iichelhadi ?

Thanks for your consideration, Ryan

Hi Ryan, Apologies. I dont have any issues running squire anymore. I am not sure what caused this issue back then. Could you post your code so I can compare to mine and see?

[AbhijeetRPatil]

@ryanmboileau One possibility for such errors would be when trying to build a STAR index for a genome and the required files are missing. In case you are also trying to build a STAR index then make sure you have set all the parameters that are required to build the index. Forex, squire Fetch -b hg38 -f -r -g -c -x -p 8

[YayanFeng]

Hi, I am already set all those parameters when I build the index. However, I am still having the same issues. Do you have found a solution ?