Andrew Lang - 2017-09-19

I have been attempting to use CASH to analyze a dataset for alternative splicing, but I am having difficulty getting the program to even read in my gtf. 

[al2025@premise isoform]$ java -jar -Xmx900m /pylon2/mc3bg6p/al2025/storage/cash_v2.1.0-alpha1/cash.jar \
> --Case:stress /mnt/lustre/macmaneslab/al2025/isoform/STAR_mappings/blu7-x_female_gonad_stress_STAR_anno_Aligned.sortedByCoord.out.bam \
> --Control:control /mnt/lustre/macmaneslab/al2025/isoform/STAR_mappings/L-G107_male_gonad_control_STAR_anno_Aligned.sortedByCoord.out.bam \
> --GTF /mnt/lustre/macmaneslab/al2025/isoform/genome_compare/Columba_livia_1.0.gtf \
> --Output /mnt/lustre/macmaneslab/al2025/isoform/CASH_out
cash version 2.1.0-alpha1
2017-09-19 15:58 [runtime:0ms] [com.novelbio.nbcgui.controlseq.CtrlSplicing:main]-[INFO] Start reading gtf file /mnt/lustre/macmaneslab/al2025/isoform/genome_compare/Columba_livia_1.0.gtf
 java.lang.NullPointerException
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGeneAbs.getMapName2Detail(GffHashGeneAbs.java:152)
    at com.novelbio.listOperate.ListHashSearch.ReadGffarray(ListHashSearch.java:247)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGeneAbs.ReadGffarray(GffHashGeneAbs.java:50)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGene.read(GffHashGene.java:187)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGene.<init>(GffHashGene.java:90)
    at com.novelbio.nbcgui.controlseq.CtrlSplicing.mainCmd(CtrlSplicing.java:355)
    at com.novelbio.nbcgui.controlseq.CtrlSplicing.main(CtrlSplicing.java:67)
Exception in thread "main" com.novelbio.analysis.seq.genome.ExceptionNbcGFF: GffFile Formate Error:/mnt/lustre/macmaneslab/al2025/isoform/genome_compare/Columba_livia_1.0.gtf
    at com.novelbio.listOperate.ListHashSearch.ReadGffarray(ListHashSearch.java:255)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGeneAbs.ReadGffarray(GffHashGeneAbs.java:50)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGene.read(GffHashGene.java:187)
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGene.<init>(GffHashGene.java:90)
    at com.novelbio.nbcgui.controlseq.CtrlSplicing.mainCmd(CtrlSplicing.java:355)
    at com.novelbio.nbcgui.controlseq.CtrlSplicing.main(CtrlSplicing.java:67)
Caused by: java.lang.NullPointerException
    at com.novelbio.analysis.seq.genome.gffOperate.GffHashGeneAbs.getMapName2Detail(GffHashGeneAbs.java:152)
    at com.novelbio.listOperate.ListHashSearch.ReadGffarray(ListHashSearch.java:247)
    ... 5 more

my gtf file is formatted as follows

NC_013978.1 RefSeq  exon    1   69  .   +   .   transcript_id "rna19564";
NC_013978.1 RefSeq  exon    70  1042    .   +   .   transcript_id "rna19565";
NC_013978.1 RefSeq  exon    1043    1114    .   +   .   transcript_id "rna19566";
NC_013978.1 RefSeq  exon    1115    2700    .   +   .   transcript_id "rna19567";
NC_013978.1 RefSeq  exon    2701    2774    .   +   .   transcript_id "rna19568";
NC_013978.1 RefSeq  CDS 2786    3751    .   +   0   transcript_id "gene15879"; gene_id "gene15879"; gene_name "ND1";
NC_013978.1 RefSeq  exon    3769    3839    .   +   .   transcript_id "rna19569";
NC_013978.1 RefSeq  exon    3845    3915    .   -   .   transcript_id "rna19570";
NC_013978.1 RefSeq  exon    3915    3983    .   +   .   transcript_id "rna19571";
NC_013978.1 RefSeq  CDS 3984    5023    .   +   0   transcript_id "gene15880"; gene_id "gene15880"; gene_name "ND2";
NC_013978.1 RefSeq  exon    5024    5094    .   +   .   transcript_id "rna19572";
NC_013978.1 RefSeq  exon    5096    5164    .   -   .   transcript_id "rna19573";
NC_013978.1 RefSeq  exon    5167    5239    .   -   .   transcript_id "rna19574";
NC_013978.1 RefSeq  exon    5242    5308    .   -   .   transcript_id "rna19575";
NC_013978.1 RefSeq  exon    5308    5379    .   -   .   transcript_id "rna19576";

Any insight into what I am doing wrong?