Problem in running spada

[Anita Tripathi]

Dear sir,

I'd installed all the required dependencies by following installation instructions specified on your wiki page, and I tried running the example files, but I am no able to run spada script as,  it is not recognising any of the spada options not even "--help", and in the spada folder I could not find "cfg.txt" file in place of this 3 othere files named cfg.crp.txt, cfg.prp.txt, and cfg.sph.txt were there which are not mentioned in "Usage" tutorials, even though I tried using these files as cfg file by changing the paths to my path as specified in tutorials

say for example

perl spada.pl --cfg cfg.crp.txt   --dir spada.crp.test   --hmm hmm.crp   --fas test/01_refseq.fa   --gff test/51_gene.gff   --org Athaliana   --sp   --threads 2


Error is:

Unknown option: dir
Unknown option: hmm
Unknown option: sp
Unknown option: threads

-----------------------------------------------------------------------

I also tried another way by skipping following command of spada installation:

"git checkout 6cfeb340e9c6312df8adefbca938ae4e41cf2e02"

Then I am getting cfg.txt file, and it is recognising all the options, but the error I am getting here is some thing different.

spada.pl --cfg cfg.txt --dir spada.crp.test/ --hmm hmm.crp/ --fas test/01_refseq.fa --gff test/51_gene.gff --org Athaliana --sp --threads 2

Error is:
Possible precedence issue with control flow operator at /usr/local/lib/perl5/site_perl/5.22.1/Bio/DB/IndexedBase.pm line 791.
=====  setting up environment variables  =====
  using Athaliana matrix
Can't use string ("HASH(0x4073058)") as a HASH ref while "strict refs" in use at /home/sb102/Anita/Chandrakant/spada_soft/spada/ConfigSetup.pm line 87, <FH> line 37.

Sir, kindly help me with this as I am struggling with this since a month, and it is really important.

[Peng Zhou]

Hi, 

Sorry to hear that the package is not working for you. I would suggest checking out the latest code first:

git pull

Then make sure the necessary perl modules were installed. For example, the first error you got (unknown option: dir...) was because the perl module "Getopt::Long" was not installed.

As for the configuration file, there is only one file (cfg.txt) which is needed to run the pipeline and available in the latest release. 

Let me know,

Best,

Peng,

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Good Day!

[Clarissa B.]

I am having the same issue:

Possible precedence issue with control flow operator at /usr/local/lib/perl5/site_perl/5.22.1/Bio/DB/IndexedBase.pm line 791.

Any solution to it? I installed all perl modules.

Thanks