labrat9

Thanks for your reply. Please find below the whole line. AF069752 1438 . T C 228 . DP=981;VDB=2.15032e-10;SGB=-0.693147;RPB=0.968173;MQB=0.321974;MQSB=0.397088;BQB=0.0320424;MQ0F=0;AC=2;AN=2;DP4=7,0,447,123;MQ=57 GT:PL 1/1:255,255,0

We have the same issue where nullarbor stopped at the assembly step. We had to manually invoke make several times to complete the pipeline. Our coverage is over 100 fold....

@remsch I have the same issue, did you manage to resolve this?

@remsch I tried several things like downgrading my samtools to v1.9 and python to 3.6 but only managed to bypass the issue when I switched off the correction step and...