#######################################################################################
#######################################################################################
### Using ref_GRCm38.p1_top_level.gff3    or       ref_GRCm38.p1_scafolds.gff3      ###
#######################################################################################
#######################################################################################
[t.lawson@utah rDiff]$ /NGS/Software/rDiff-master/bin/rdiff -o /NGS/users/Thomas/rDiff/output2/ -d /NGS/users/Thomas/rDiff/ -a wt_7.bam,wt_8.bam,wt_203.bam -b mut_2.bam,mut_201.bam,mut_204.bam -g /NGS/users/Thomas/Transcripts/ref_GRCm38.p1_top_level.gff3 -m param -L 51 -m 30
%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

Writting results to: /NGS/users/Thomas/rDiff/output2/
1a. load the genome annotation in GFF3 format, create an annotation object
Traceback (most recent call last):
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 532, in <module>
    __main__()
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 523, in __main__
    genes, transcripts, exons, utr3, utr5, cds = GFFParse(gff_file)
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 441, in GFFParse
    for fid in gid.split(','): # child may be mapped to multiple parents ex: Parent=AT01,AT01-1-Protein
AttributeError: 'NoneType' object has no attribute 'split'


#######################################################################################
#######################################################################################
### Using gffread GTF/GFF file conversion tool on ensembl GTF from UCSC             ###
#######################################################################################
#######################################################################################
[t.lawson@utah rDiff]$ /NGS/Software/rDiff-master/bin/rdiff -o /NGS/users/Thomas/rDiff/output/ -d /NGS/users/Thomas/rDiff/ -a wt_7.bam,wt_8.bam,wt_203.bam -b mut_2.bam,mut_201.bam,mut_204.bam -g /NGS/users/Thomas/Transcripts/ensemblGenes_from_UCSC_GFFREAD.gff3 -m param -L 51 -m 30
%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

Writting results to: /NGS/users/Thomas/rDiff/output/
1a. load the genome annotation in GFF3 format, create an annotation object
Traceback (most recent call last):
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 532, in <module>
    __main__()
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 523, in __main__
    genes, transcripts, exons, utr3, utr5, cds = GFFParse(gff_file)
  File "/NGS/Software/rDiff-master/bin/../tools/ParseGFF.py", line 441, in GFFParse
    for fid in gid.split(','): # child may be mapped to multiple parents ex: Parent=AT01,AT01-1-Protein
AttributeError: 'NoneType' object has no attribute 'split'


#######################################################################################
#######################################################################################
### Using GFF Toolkit on ensembl GTF from UCSC       			            ###
#######################################################################################
#######################################################################################
/NGS/Software/rDiff-master/bin/rdiff -o /NGS/users/Thomas/rDiff/output/ -d /NGS/users/Thomas/rDiff/ -a wt_7.bam,wt_8.bam,wt_203.bam -b mut_2.bam,mut_201.bam,mut_204.bam -g /NGS/users/Thomas/Transcripts/Galaxy7-\[GTF_to_GFF3_on_data_6\].gff3 -m param -L 51 -m 30
%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

Writting results to: /NGS/users/Thomas/rDiff/output/
1a. load the genome annotation in GFF3 format, create an annotation object
warning: X11 DISPLAY environment variable not set

Compute index for the bam files
Indexing /NGS/users/Thomas/rDiff/wt_7.bam
/NGS/users/Thomas/rDiff/wt_7.bam already indexed
Indexing /NGS/users/Thomas/rDiff/wt_8.bam
/NGS/users/Thomas/rDiff/wt_8.bam already indexed
Indexing /NGS/users/Thomas/rDiff/wt_203.bam
/NGS/users/Thomas/rDiff/wt_203.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_2.bam
/NGS/users/Thomas/rDiff/mut_2.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_201.bam
/NGS/users/Thomas/rDiff/mut_201.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_204.bam
/NGS/users/Thomas/rDiff/mut_204.bam already indexed

%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2. Differential testing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%

warning: X11 DISPLAY environment variable not set
Set the paths
Load configuration
Compute regions common to multiple genes
Compute alternative regions
Measure gene expression
Getting gene expression for: /NGS/users/Thomas/rDiff//wt_7.bam
[bam_parse_region] fail to determine the sequence name.
Invalid region chr5_JH584299_random:806210-809281
error: memory exhausted or requested size too large for range of Octave's index type -- eval failed


#######################################################################################
#######################################################################################
### Using GFF Toolkit on ensembl GTF from NCBI       			            ###
#######################################################################################
#######################################################################################
[t.lawson@utah Transcripts]$ /NGS/Software/rDiff-master/bin/rdiff -o /NGS/users/Thomas/rDiff/output/ -d  /NGS/users/Thomas/rDiff/ -a wt_7.bam,wt_8.bam,wt_203.bam -b mut_2.bam,mut_201.bam,mut_204.bam -g /NGS/users/Thomas/Transcripts/genes_mm10_galaxy_convert.gff3 -m param -L 50 -m 30
%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

Writting results to: /NGS/users/Thomas/rDiff/output/
1a. load the genome annotation in GFF3 format, create an annotation object
warning: X11 DISPLAY environment variable not set

Compute index for the bam files
Indexing /NGS/users/Thomas/rDiff/wt_7.bam
/NGS/users/Thomas/rDiff/wt_7.bam already indexed
Indexing /NGS/users/Thomas/rDiff/wt_8.bam
/NGS/users/Thomas/rDiff/wt_8.bam already indexed
Indexing /NGS/users/Thomas/rDiff/wt_203.bam
/NGS/users/Thomas/rDiff/wt_203.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_2.bam
/NGS/users/Thomas/rDiff/mut_2.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_201.bam
/NGS/users/Thomas/rDiff/mut_201.bam already indexed
Indexing /NGS/users/Thomas/rDiff/mut_204.bam
/NGS/users/Thomas/rDiff/mut_204.bam already indexed

%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2. Differential testing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%

warning: X11 DISPLAY environment variable not set
Set the paths
Load configuration
Compute regions common to multiple genes
Compute alternative regions
Measure gene expression
Getting gene expression for: /NGS/users/Thomas/rDiff//wt_7.bam
error: convert_reads_to_region_indicators: A(I,J): column index out of bounds; value 11054 out of bound 7483
error: called from:
error:   /NGS/Software/rDiff-master/src/tools/convert_reads_to_region_indicators.m at line 16, column 19
error:   /NGS/Software/rDiff-master/src/get_reads_caller.m at line 71, column 48
error:   /NGS/Software/rDiff-master/src/get_read_counts.m at line 32, column 17
error:   /NGS/Software/rDiff-master/src/rdiff.m at line 38, column 5
starting Octave failed