Dear Developers,
After running my 20 genomes with the Markers Discovery pipeline around a 100 times (trying different parameters combos), I always ended with the same result: "No markers identified"
Even with genomes belonging to the same species, the pipeline find nothing. Another weird thing that happens is that the whole analysis takes between 0 to 3 secs, so no mapping step is happening I guess. Also I always get this flag:
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Get FASTQ files of the contigs generated %%%%%%%%%%%%%%%%%%%%%%%%%%%
Which doesnt make sense as started the fasta assemblies from SPAdes, and also tried converting these fastas to .fq, but I still get that.
an example of parameters im using :
-VD -1 -CL 1 -VL 10 -CD 50 -SLCD 1e-05 -MCT 1 -rdgopen 5 -rdgexten 3 -mp 4 -max_SoftClipping 10 -MPA 0.1 -SI 50 -p 28
output example :
#################################################################################################
#################################### Mapping Process started ####################################
#################################################################################################
[ System Call: perl /zgrouphome/fslg_Lecanomics/DOMINO/bin/scripts/DM_MappingReads.pl /lustre/scratch/grp/fslg_Lecanomics/DOMINO_outputs 1600790935 ]
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Get FASTQ files of the contigs generated %%%%%%%%%%%%%%%%%%%%%%%%%%%
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++ Analysis of Molecular Markers started +++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Markers Directory: /lustre/scratch/grp/fslg_Lecanomics/DOMINO_outputs/202009221008_DM_markers ...OK
[ Tue Sep 22 10:08:56 2020 ] Step took 00 hours, 00 minutes, and 01 seconds
#################################################################################################
##################################### No markers identified #####################################
#################################################################################################
+ Termination of DOMINO marker identification
+ No markers were identified using these parameters...
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++ ANALYSIS FINISHED +++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[ Tue Sep 22 10:08:56 2020 ] Whole process took 00 hours, 00 minutes, and 01 seconds
Early termination, exiting the script
please help!
Cristóbal
Dear Developers,
After running my 20 genomes with the Markers Discovery pipeline around a 100 times (trying different parameters combos), I always ended with the same result: "No markers identified"
Even with genomes belonging to the same species, the pipeline find nothing. Another weird thing that happens is that the whole analysis takes between 0 to 3 secs, so no mapping step is happening I guess. Also I always get this flag:
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Get FASTQ files of the contigs generated %%%%%%%%%%%%%%%%%%%%%%%%%%%Which doesnt make sense as started the fasta assemblies from SPAdes, and also tried converting these fastas to .fq, but I still get that.
an example of parameters im using :
-VD -1 -CL 1 -VL 10 -CD 50 -SLCD 1e-05 -MCT 1 -rdgopen 5 -rdgexten 3 -mp 4 -max_SoftClipping 10 -MPA 0.1 -SI 50 -p 28output example :
please help!
Cristóbal