Hello mauve users, I am playing around with using mauve for a multiple alignment of a locus with rearrangements, and after some point felt that looking at gene identities in one of the genomes which is well studied was crucial for understanding the graphs. I use mauve in the graphical interface, not command line, but could switch to the latter if needed. My problem is that when I load the genbank file for the genomic region I am interested in, progressive mauve throws out this error message:
Executing: /Applications/MAUVE/Mauve.app/Contents/MacOS/progressiveMauve -- output=/Users/nat/Neurospora/Mat_Scaffolded/MAUVE/ Gb_1maiNotFullGbk.guide_tree --output-guide-tree=/Users/nat/Neurospora/ Mat_Scaffolded/MAUVE/Gb_1maiNotFullGbk.guide_tree.guide_tree -- backbone-output=/Users/nat/Neurospora/Mat_Scaffolded/MAUVE/ Gb_1maiNotFullGbk.guide_tree.backbone /Users/nat/Neurospora/ Mat_Scaffolded/crassa_notfull_sequences.gbk /Users/nat/Neurospora/ Mat_Scaffolded/crassa_Smalla.fa /Users/nat/Neurospora/Mat_Scaffolded/ A123_assembled57_Afr.fa /Users/nat/Neurospora/Mat_Scaffolded/ A123_assembled74_a_assembled302_Sub.fa /Users/nat/Neurospora/ Mat_Scaffolded/aA123_assembled228_Pan.fa /Users/nat/Neurospora/ Mat_Scaffolded/A12_assembled637_a_assembled9_Ter.fa Storing raw sequence at /var/folders/Od/Ody+O3O-F5GoO0-1x7-gC++++TI/- Tmp-/rawseq12992.000 terminate called after throwing an instance of 'std::ios_base::failure' what(): failed mapping file: Invalid argument Exited with error code: 134 I haven't found anything relevant in the archives about this error code. I checked that the genebank file is not containing any empty fields as the JGI ones that someone in the list previously had an issue with. My genbank file is loaded from NCBI. I tried with different genebank download versions (there is a full and a 'withparts' version that I am not sure what as to they differ in), explicitly giving a .gbk extension to the files, different computers (Macs of up to 4 G memory), well, nothing worked. i know this is an issue with the gbk files, because progressive mauve runs OK when i load the corresponding FasTA file instead. I am still not sure if this is a memory or size issue though: I see in my Activity monitor that he mauve I downloaded for Macs (> 10.4) is a 64-bit version,although my Macs are 32-bit architectures. Also, I think I saw somewhere that the genbank file needs to correspond to less than 1 Mb of sequence, and I have 1.3Mb of sequence. I could eventually try to find a way of extracting from the genbank file a smaller chunk, but is this really the issue? Any help would be highly appreciated! Thank you, Anastasia Gioti Post-Doc, Evolutionary Biology Department Uppsala University Norbyvägen 18D, SE-75236 UPPSALA anastasia.gi...@ebc.uu.se Tel: +46-18-471-2837 Fax:+46-18-471-6310 ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
