CeleScope error regular expression?

Describe the bug when running flv_trust4 assay, I got the error below

subprocess.CalledProcessError: Command ' awk '$4!~"_" && $4!~"?"' .//C2301003-3-T/03.assemble/assemble/C2301003-3-T_report.tsv > .//C2301003-3-T/03.assemble/assemble/C2301003-3-T_filter_report.tsv 2>&1' returned non-zero exit status 2

the awk syntax maybe <awk '"_"!~$4 && "?"!~$4'>, right? I don't know what is doing here, maybe export the line which the fourth column doesn't match an underscore and question mark, but I got this error

Version e.g. 2.1.0

Oct 23 '24 03:10 RuixiangLiu01

Seems the gawk problem. try to install gawk before running. conda install -c anaconda gawk

Oct 23 '24 05:10 Chenjunjie1996

Seems the gawk problem. try to install gawk before running. conda install -c anaconda gawk

Thanks for reply! What I used is a docker image which built use the Dockerfile in repo

Another thing is that I noticed the fourth column in file "03.assemble/assemble/{sample}_report.tsv" is amino acid sequence, and its' content maybe "out_of_frame" or contains underscore or question mark, eg: "CSV_VAGIQETQYF" or "CAVVESGNTGK?IF". I wonder know the purpose of this step is to filter out these tcr?

Oct 23 '24 06:10 RuixiangLiu01

Yes, TCRs that meet these conditions will be filtered. https://github.com/liulab-dfci/TRUST4/issues/92

Oct 23 '24 06:10 Chenjunjie1996

Yes, TCRs that meet these conditions will be filtered. liulab-dfci/TRUST4#92

Thanks, install gawk can run this command

Oct 23 '24 06:10 RuixiangLiu01