Dear Ben,
turned out that the problem was indeed the "//" separator between the profiles: when I applied 'sed' to change the path in the pssm and list files the double slash was removed, resulting in this quite obscure error.
Sorry for using your time, Marco
On 11/06/2014 21:27, Ben Webb wrote: > On 6/6/14, 5:29 AM, Marco Galardini wrote: >> thanks for your prompt reply: the problem is that the PSSM file should >> be ok. > > Looks OK. If you can send me the Modeller input file and whatever file > it's trying to read (presumably the .pssm) then I can take a look and > see if I can reproduce your problem here. (If you can cut down the > .pssm to a smaller size and still reproduce the problem, that would > help ;) - look for the // separators.) > > Ben