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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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squire Call error #78

Closed Surar closed 2 years ago

Surar commented 2 years ago

Hi, Thank you very much for the useful software, I'm trying to run squire Call on my data and I'm getting different error messages like ValueError: could not convert string to float: copies or if I used -s option I'm getting the errors below: ValueError: invalid literal for int() with base 10: 'tx_stop' ValueError: invalid literal for int() with base 10: 'Sample'

however I'm still getting the deseq, MA-plots and the combo.txt output. do I need to worry about these error messages? if yes, what do you think might be the reason?

many thanks in advance. Surar

jamesc99 commented 2 years ago

Hi,

Actually, I don't know how to run Call command in SQuIRE, could anyone give me an example about it? I really appreciate that! (totally new to ComBio

Ryan

Surar commented 2 years ago

Hi @jamesc99, I'm not the author but I'm using SQUIRE. There is an example of each command in the README.md file of the code and for the squire call its squire Call [-h] -1 <str1,str2> or -2 <str1,str2> or -A -B [-o ] [-s] [-p ] [-N ] [-f ] [-v] the options are explained in the README.md file. if you have specific question feel free to ask. Best regards Surar

Surar commented 2 years ago

Hi all,

the problem is solved by providing a basename shared for the samples in a specific condition and not a list for all of them.