Error while running Call step

[AbhijeetRPatil]

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]) to milliDiv = int(float(line[12])). However, I still keep getting error.

[fernandogs97]

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]) to milliDiv = 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?

[AbhijeetRPatil]

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.

[fernandogs97]

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)

[imtiyazhariyani]

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.