Specifying multiple .fasta reference genomes?

[chklovski]

I'm trying to run metacompass, and it runs fine if I specify a single reference .fasta genome with -r, but cannot recognize multiple .fasta genomes, and crashes if I provide it with a .fasta file containing all the reference genomes in a single file. Is it possible to run MetaCompass with multiple .fasta reference genomes?

[vcepeda]

The file is assumed to be multi-fasta.

[chklovski]

Are there any requirements? Blank line between different organisms or between contigs, sequence line length, anything else? Whenever I provide metacompass a multi-fasta file, it invariably crashes during the contig_build job with a segmentation fault exception, but runs fine if provided an individual genome .fasta.

[vcepeda]

Please provide the error and the headers of your muti and single fasta files.

[chklovski]

Sorry! It was my fault. I had two contigs in the merged fasta with identical headers. Unique headers fixed the problem.