Closed AbhijeetRPatil closed 3 years ago
I am trying to run SquiRE call. However, I am getting errors. I have attached the error below. Could anyone please help me fix the error.
Script Arguments
count_folder=/home/arpatil/TE_counts projectname=TEs_T1D_Normal_Squire output_format=pdf pthreads=12 call_folder=/home/arpatil/dete condition2=Normal tableonly=False group1=T1D func=<function main at 0x7fa278b34140> group2=Normal_ subfamily=False verbosity=True condition1=T1D
Traceback (most recent call last): File "/home/arpatil/miniconda3/envs/squire/bin/squire", line 11, in load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/home/arpatil/Tools/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/home/arpatil/Tools/SQuIRE/squire/Call.py", line 286, in main create_TE_dict(TE_combo,TE_dict,threshold) File "/home/arpatil/Tools/SQuIRE/squire/Call.py", line 134, in create_TE_dict milliDiv = int(line[12]) ValueError: invalid literal for int() with base 10: 'Sample'
I tried editing Call.py line 134 by changing
milliDiv = int(line[12])
tomilliDiv = int(float(line[12]))
. However, I still keep getting error.
Hello, Can you write here the code of Call that you have written in the bash?
Hello, thanks for your response.
squire Call -i $CountDir -1 RNA_seq_T1D_* -2 RNA_seq_Normal_* -A T1D -B Normal -o ${deteDir} -p 4 -N TEs_T1D_Normal_Squire -f pdf -v
The parameters for -1 and -2 are common patterns of case and control files.
Hello, thanks for your response.
squire Call -i $CountDir -1 RNA_seq_T1D_* -2 RNA_seq_Normal_* -A T1D -B Normal -o ${deteDir} -p 4 -N TEs_T1D_Normal_Squire -f pdf -v
The parameters for -1 and -2 are common patterns of case and control files.
I don't see any error, have you tried to perfome the call step without using the regular expression? Maybe it could be the reason of the error. (Just an idea)
Hi there, I'm getting the same error and was wondering how you solved it? I see this error regardless of whether I use the regular expression or common patterns.
I am trying to run SquiRE call. However, I am getting errors. I have attached the error below. Could anyone please help me fix the error.
Script Arguments
count_folder=/home/arpatil/TE_counts projectname=TEs_T1D_Normal_Squire output_format=pdf pthreads=12 call_folder=/home/arpatil/dete condition2=Normal tableonly=False group1=T1D func=<function main at 0x7fa278b34140> group2=Normal_ subfamily=False verbosity=True condition1=T1D
Traceback (most recent call last): File "/home/arpatil/miniconda3/envs/squire/bin/squire", line 11, in
load_entry_point('SQuIRE', 'console_scripts', 'squire')()
File "/home/arpatil/Tools/SQuIRE/squire/cli.py", line 156, in main
subargs.func(args = subargs)
File "/home/arpatil/Tools/SQuIRE/squire/Call.py", line 286, in main
create_TE_dict(TE_combo,TE_dict,threshold)
File "/home/arpatil/Tools/SQuIRE/squire/Call.py", line 134, in create_TE_dict
milliDiv = int(line[12])
ValueError: invalid literal for int() with base 10: 'Sample'
I tried editing Call.py line 134 by changing
milliDiv = int(line[12])
tomilliDiv = int(float(line[12]))
. However, I still keep getting error.