When a bad genome fails to be aligned to the ref with progressiveMauve a WARNING is prompted to stdout. It would be an improvement if the name of the genome and the reference that fails is added in this warning.
Example how the looks now. Here it fails for all 5 references but there is hard to know which ref and which genome that is concerned.
2020-04-20 10:24:18,723 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2020-04-20 10:24:18,724 CanSNPer2 [WARNI] This progressiveMauve error is showing up for bad genomes containing short repetative contigs
2020-04-20 10:24:18,726 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2020-04-20 10:24:18,726 CanSNPer2 [WARNI] This progressiveMauve error is showing up for bad genomes containing short repetative contigs
2020-04-20 10:24:18,727 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2020-04-20 10:24:18,727 CanSNPer2 [WARNI] This progressiveMauve error is showing up for bad genomes containing short repetative contigs
2020-04-20 10:24:18,729 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2020-04-20 10:24:18,729 CanSNPer2 [WARNI] This progressiveMauve error is showing up for bad genomes containing short repetative contigs
2020-04-20 10:24:18,731 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2020-04-20 10:24:18,731 CanSNPer2 [WARNI] This progressiveMauve error is showing up for bad genomes containing short repetative contigs
14VLT651o6: NA
When a bad genome fails to be aligned to the ref with progressiveMauve a WARNING is prompted to stdout. It would be an improvement if the name of the genome and the reference that fails is added in this warning.
Example how the looks now. Here it fails for all 5 references but there is hard to know which ref and which genome that is concerned.