mehuljani/islandcafe

:flags: :ocean: CAFE is a genomic island Prediction tool

islandcafe's Issues

No clusters with example data

When running the example, I get the following error:

$ ./cafe -phylo -genus bartonella -gbk example.gbk


Building a new DB, current time: 09/25/2018 12:17:13
New DB name:   /home/nicholas/GitHub/CAFE/faa_database
New DB title:  faa_database
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 7095 sequences in 0.29547 seconds.
No Genomic islands detected
rm: cannot remove 'CAFE_temp': No such file or directory

Looking at cafe, it appears that around lines 386 and 393 are commenting out the call to cafe.out.

I think I have the fix, so I'll submit a pull request, but if I'm off base please do let me know!

Thanks in advance,

~Nick

Cannot open input file: No such file or directory at cgview_xml_builder.pl line 1820.

I found out the cafe did not write the CAFE.fna file in the folder so that the required input CAFE.fna of the cgview_xml_builder.pl was missing, which gave out the the error of : Cannot open input file: No such file or directory at cgview_xml_builder.pl line 1820.

system ("perl cgview_xml_builder.pl -sequence $in_filename)
$in_filename should be "$name_CAFE.fna", if my input file and ouput file were not in the same place.

I am not familar with perl code, so I did the following simple revision of the code:

$wrong_path=$infile . "_CAFE.fna";
$correct_path="$name\_CAFE.fna";
system ("mv $wrong_path $correct_path");

And this revision work fine for me.

Phlylogenetic module

Hi! Thank you very much for your software, so far it has worked well for me.
I wanted to ask you if you could explain to me briefly how to make the phylogenetic module option work, I really don't understand it and I would appreciate an explanation of its use in order to do a better job.

Thank you in advance

Sven

Testing with sample data did not work

I use this line:
./cafe -phylo -genus bartonella -gbk example.gbk --verbose

The output was:
2487641 2488298 0.060222165473
2485102 2487640 0.017415755062
2488299 2489200 0.044747224651
Clustering...
It is almost done now
Undefined subroutine &main::abs_path called at ./cafe line 400, line 47389.