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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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run_salmon_fq and EXPR.csv file not found error #37

Closed shreya1704 closed 4 years ago

shreya1704 commented 4 years ago

I am using SalmonTE 0.4 with default quant function and getting following error.

Screen Shot 2019-08-12 at 5 18 30 PM
hyunhwan-jeong commented 4 years ago

Hello @shreya1704,

Thank you,

Hyun-Hwan Jeong

shreya1704 commented 4 years ago

Hi Hyun-Hwan,

  1. I was just running SalmonTE.py quant --reference=hs example when I got the error.

  2. Screen Shot 2019-08-13 at 10 27 58 AM

Thanks.

hyunhwan-jeong commented 4 years ago

Please follow the instruction below (this is from README.md);

Q. I am using SalmonTE on macOS and salmonTE fails to run on quant mode with error messages:

CalledProcessError in line xx of SOME_PATH:
Command ' set -euo pipefail;  ROOT_OF_SALMON_TE/SalmonTE/salmon/darwin/bin/salmon quant...' returned non-zero exit status 134.

A. You may have a problem to run salmon which is an essential tool for the pipeline. You may install Threading Building Blocks library to solve the problem. If you are using homebrew then please use below command:

brew install tbb

Best,

Hyun-Hwan Jeong

shreya1704 commented 4 years ago

It is working now. Thank you