Quit during trimal - "composed only by gaps" error

[guyleonard]

WARNING: Removing sequence '576696987' composed only by gaps

WARNING: Output alignment has not been generated. It is empty.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can not open '/storage/home/aurelie/hypho_orthoMCL_tree/hypho_node_60_66_orthologues/masks/hyc3ortho122514_hits.afa-tr' for reading: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::Tools::GuessSeqFormat::guess /usr/share/perl5/Bio/Tools/GuessSeqFormat.pm:464
STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:395
STACK: main::mask_check orchard.pl:368
STACK: main::run_trimal orchard.pl:356
STACK: main::masking_step orchard.pl:309

STACK: orchard.pl:181

This appears if the "-nogaps" option runs and does not produce a file... perhaps it would just be easier to go with "-automated1" all the time...