FAQ - Reported issues and solutions

In some cases, SMuFin does not find any valid BWT index for the reference genome

Conflicts with the indexing of some reference genome sequences and BWA libraries used by SMuFin can occur. In this case, the program reports:

Checking input data files... No BWT index found for [reference_genome.fasta]. Generating index... [bwa_index] Pack FASTA... *** Process received signal *** Signal: Segmentation fault (11) To solve this problem, either use the reference genome (hg19) provided here, or index your own reference using the index command within BWA version 0.7.X or above. Indexing using previous versions of BWA is not compatible with current version of SMuFin.

The replication of a SMuFin execution gives different results on the same data set using a different number of nodes

Eventually, when replicating a SMuFin execution on the same data set using different number of nodes or in different environments, small (1 in 1000) discrepancies of nucleotide sequence around large SV breakpoints can occur. This does not affect the results or the accuracy of somatic variant detection and is due to the alternative selection of different allele versions of a particular germline variant present in heterozygosis in the tumor genome.

Is it possible to execute SMuFin in a single node?

Yes, you can execute SMuFin using only one node. However, you must submit a job using MPI and requiring into your queuing system just one full node and enabling at least two processes (-np 2) in the command line. In this way these two MPI processes will be executed in the same node. Please, make sure that the available RAM memory in the node is enough to run the application.