java -jar CIRI_Full_v2.1.1.jar Merge

[Thananonsr]

Hello everyone,
I’ve been analyzing circRNAs data from RNA sequencing using CIRI2 tools, with a total of 18 samples (running one sample at a time).
The issue I’m encountering now is when I run the following command:
*java -jar CIRI_Full_v2.1.1.jar Merge
-c SRR19666460/rawdata/SRR19666460.ciri
-as SRR19666460/rawdata/SRR19666460_jav.list
-ro SRR19666460/rawdata/SRR19666460_ro2_info.list
-a gencode.v46.annotation.gtf
-r bwa.index_hg38.fa/hg38.fa
-o SRR19666460/rawdata *
unset DISPLAY
classpath = /
Output prefix = /workshop/SRR19666460/rawdata

Merge module start

Loading Annotation...
Annotation Loaded
Loading CIRI_AS output...
CIRI_AS output Loaded
Loading CIRI output...
CIRI output Loaded
Loading CIRI_RO output...
CIRI_RO output Loaded
Combine AS and RO output
Combine completed, 7 reads are used
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.util.List.iterator()" because "this.gtflist" is null
at Exon_gtf.get_exon(Exon_gtf.java:16)
at Merge3.getmerge(Merge3.java:789)
at CIRI_Full2.main(CIRI_Full2.java:555)

I’m getting the error message:
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.util.List.iterator()" because "this.gtflist" is null
at Exon_gtf.get_exon(Exon_gtf.java:16)
at Merge3.getmerge(Merge3.java:789)
at CIRI_Full2.main(CIRI_Full2.java:555)
This is preventing me from continuing with my analysis. The issue only occurs with one of the samples. Despite my efforts to troubleshoot, I haven’t been able to resolve it. I would appreciate any help from you all.