When I run parSNP on 14 genomes with a random reference genome, the output file only includes 12 of them. I am using parSNP with the -c command. I have tried to circumvent the problem by forcing the program to use one of the dropped genomes as the reference (using -r). The error I receive is:
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
ERROR
The following command failed:
/tmp/_MEIIrMqqu/parsnp /path/to/my/directory//parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
ERROR
Can you help me determine what is going on? It seems like the two genomes that are removed are random.
Hi,
When I run parSNP on 14 genomes with a random reference genome, the output file only includes 12 of them. I am using parSNP with the -c command. I have tried to circumvent the problem by forcing the program to use one of the dropped genomes as the reference (using -r). The error I receive is: -->Running Parsnp multi-MUM search and libMUSCLE aligner.. ERROR The following command failed:
Can you help me determine what is going on? It seems like the two genomes that are removed are random.
Thanks.