running Juicer "awk: syntax error"

Question

[Jarjayes]

I'm using Juicer to analyze Hi-C data.

I finished install and try to use test data.

When I run

It seems to "chimeric_sam.awk" has a problem. I'm beginner of bioinformatics. Can anyone help me ?

[Matthias Zepper]

Yes, Juicer and Juicebox are notoriously fickly to get to run. I recommend using a Docker container (e.g. this one) to save yourself some hassle.

In your particular case, I think the problem is the macOS version of awk. macOS is a derivative of BSD, whereas most Linux distributions package components of the GNU operating system together with the Linux kernel. (For this reason, a bitter dispute ignited over whether naming it GNU/Linux would be more appropriate). Many utility tools such as grep, sed, awk have been notably improved from their original Unix versions by the GNU developers. Thus, the versions shipped with most Linux distributions are superior to those contained in macOS. (e.g. the macOS grep doesn’t support Lookarounds or the match reset \K in regexes.). Since the Docker image is based on Linux, things should work there.

[Jarjayes]

Thank you.　 I have not used Docker, but taking this opportunity, I will try to use.

I will ask questions if I there is something that I don't understand.