JFsanchezherrero
commented
7 years ago Dear Adam, Let's go one step at a time.
Experimental keys on scalar is forbidden at...: I am afraid what you mention here is a problem due to the perl version o subversion at the moment of traversing the hash of hashes. I will try to check it out and fix it in further DOMINO versions.
SAMTOOLS installation Sometimes some third party software included in DOMINO might fail during the installation and the thing is we are not dealing with it. It would definitely be really useful to include some kind of mini-test just to check everything is installed fine before running DOMINO.
DOMINO parameters I am afraid the error you can see here is due to the parameter configuration. I have to admit the example test files we use here are not fully profitable. They are real data from a set of markers we develop for another project, but sometimes, taking into account the parameters it might not provide markers.
I suggest you can use the simulated files we generated to test the efficiency and sensitivity of DOMINO which are under: DOMINO/example/simulated_data/
If you want to try with the real data you can set parameters to:
-VD 0.01 -CL 40 -VL 400 -CD 1 -DM discovery -MCT 3:
--> MCT: minimum covered taxa: it means at least 3 taxa would be fulfilling parameters.
-VD -1 -CL 40 -VL 400 -CD 1 -DM discovery --> VD -1: it would retrieve any marker with a positive divergence (greater than 0)
I suggest you use a fix integer for the CL and VL parameters. We are working in the range set for these parameteres and we will be updating DOMINO soon.
Thank you very much for your interest, please contact me for any further questions.
Jose F. Sanchez
entobento
I have come across the "Experimental keys on scalar is now forbidden at <lines 2988, 3009, and 3028>" error in the DM_MarkerScan_V1.0.2.pl script. I have corrected it by changing the code from foreach <my $x (keys $y{$z}> to <foreach my $x (keys %{ $y{$z} }> It seems to run okay but the script then fails throwing the error:
ERROR: Can not open folder ... DOMINO/bin/lib/DOMINO.pm line 510.
The problem here seems to be that samtools 1.3.1 didn't fully install. I install/make samtools version 1.3.1 and placed it in the DOMINO/bin file.
Now it seems to run well... but it spits out this error no matter what parameters I use:
+ Generate a BLAST database... Generating the database failed when trying to proccess the file... DOMINO would not stop in this step... !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Early termination of the DOMINO Marker Scan... Please note that DOMINO could not find any markers for the parameters provided. Please Re-Run DOMINO using other parameters
To test and run DOMINO I'm using the 454 reads and the various input options specified below: perl bin/DM_MarkerScan_v1.0.2_corr.pl -option DOMINO_files $HOMEDIR"201708311418_DM_assembly" -o $HOMEDIR -type_input single_end -taxa_names Nemesia_sp043,N_raripilia061,N_raripilia079,I_brauni098 -VD 0.01 -CL 20::100 -VL 100::500 -CD 1 -DM discovery
Is this latter error an actual error or a parameter input problem?
Thanks for any guidance, Adam