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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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NameError in line 24 of /SalmonTE-master/snakemake/Snakefile.paired: name 'directory' is not defined #67

Closed Gemma-Zhang-326 closed 2 years ago

Gemma-Zhang-326 commented 2 years ago

Hi I am trying to use SalmonTE, but encounter an issue when testing with the example data. Could help me check this? Many thanks!

(SalmonTE) SalmonTE-master$ python SalmonTE.py quant --reference=hs ./example 2022-05-17 10:23:58,042 Starting quantification mode 2022-05-17 10:23:58,042 Collecting FASTQ files... 2022-05-17 10:23:58,042 SalmonTE assumes that './example/' is a directory, and SalmonTE will search any FASTQ file in the directory. 2022-05-17 10:23:58,043 The input dataset is considered as a paired-ends dataset. 2022-05-17 10:23:58,044 Collected 4 FASTQ files. 2022-05-17 10:23:58,044 Quantification has been finished. 2022-05-17 10:23:58,044 Running Salmon using Snakemake NameError in line 24 of /SalmonTE-master/snakemake/Snakefile.paired: name 'directory' is not defined File "/SalmonTE-master/snakemake/Snakefile.paired", line 24, in 2022-05-17 10:23:58,124 NameError in line 24 of /SalmonTE-master/snakemake/Snakefile.paired: name 'directory' is not defined File "/Salmon/SalmonTE-master/snakemake/Snakefile.paired", line 24, in Traceback (most recent call last): File "SalmonTE.py", line 292, in run(args) File "SalmonTE.py", line 243, in run run_salmon(param) File "SalmonTE.py", line 156, in run_salmon with open(os.path.join(param["--outpath"], "EXPR.csv" ), "r") as inp: FileNotFoundError: [Errno 2] No such file or directory: '/Salmon/SalmonTE-master/SalmonTE_output/EXPR.csv'

Gemma

Gemma-Zhang-326 commented 2 years ago

I find out this bugs due to the version of snakemake is too old. The problem is solved when I update snakemake to 7.6.2 Thank you!