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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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How to run "squire Call" #65

Closed mars188 closed 2 years ago

mars188 commented 2 years ago

Hello,

This may be a trivial one but I can't get the squire Call run with two groups of samples. Here is how my code looks like:

squire Call --group1 data_analysis/squire_count/Liv1_Hi272_Mut_* -2 data_analysis/squire_count/Liv2_Hi272_Cont_* -A mutant -B control -o data_analysis/squire_call/ -p 24 -v

The "squire_count" folder contains all the count file:

Then I get the following error:

Traceback (most recent call last): File "/scratch/gencore/conda3/envs/squire/bin/squire", line 11, in <module> load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/scratch/gencore/ma5877/TE/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/scratch/gencore/ma5877/TE/SQuIRE/squire/Call.py", line 270, in main group1_list=get_groupfiles(group1,gene_files,subF_files,TE_files,subfamily,count_folder) File "/scratch/gencore/ma5877/TE/SQuIRE/squire/Call.py", line 88, in get_groupfiles TE_files.append(find_file(count_folder,"_TEcounts.txt",sample,1,True)) File "/scratch/gencore/ma5877/TE/SQuIRE/squire/Call.py", line 43, in find_file raise Exception("No " + pattern + " file") Exception: No _TEcounts.txt file

But "_TEcounts.txt" file is there in the "squire_count" folder. Am I providing the wrong script? Please help!

mars188 commented 2 years ago

Ok I have solved the issue. It requires "-i" option for count folder that was not mentioned in the manual but if you do squire Call --help then it shows all the option including that "-i".