Detecting Minor SNV - Missing $autopar variable

[iek]

Hi Dr. Feng, when detecting minor SNVs, the program runs but does show a message of "igda_pipe_detect_ont: line 114: [: missing `]'". I looked into line 114 of igda_pipe_detect_ont, and it calls a $auto_par variable that is set to $OPTARG. Do you know what this error message is saying? I thought I inputted all required variables, and the program seems to be running smoothly, but I wanted to make sure. Thank you so much!

[zhixingfeng]

Hi iek,
$auto_par is a parameter reserved for internal testing, and should have a valid default value 1 if the user doesn't set "-a" in "igda_pipe_detect_ont". Could you please send me your full command line or a minimal example data if possible so that I could reproduce the error? Thank you very much.

BTW, does the example Nanopore dataset work in your machine? It is at https://www.dropbox.com/sh/umi03t3eendcktf/AABhXy2cNfQAr0wBike87Kc0a?dl=0 (the ont_kpneumoniae folder)

[iek]

Hi Dr. Feng,

Would it be okay if I sent you an email with the information (to the address you have listed in your Github)? Thank you so much.

[zhixingfeng]

Yes, please send them to zxfeng.thu@gmail.com.

[iek]

Thank you! I just sent you an email.