Java error when running java -jar /apps/ciri/2.1.1/bin/CIRI_Full_v2.1.1.jar Pipeline

[SimoneRossi94]

Hello,

I am trying to run the CIRI full jar in Pipeline mode and it goes smoothly until the merge part, in particular, the CIRI-AS part creates the folder output but does not write any file inside of it.
I have attached the files of stderr and stdout below.

CIRI_stderr.txt
CIRI_stdout.txt

Exception in thread "main" java.io.FileNotFoundException: /data/data_storage/novaseq_results/research/circRNA_Medulloblastoma/CIRI_outputs/ICGC_MB50/CIRI-AS_output/CIRI_output_jav.list (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
at java.base/java.io.FileInputStream.(FileInputStream.java:157)
at java.base/java.io.FileInputStream.(FileInputStream.java:111)
at java.base/java.io.FileReader.(FileReader.java:60)
at Merge3.getmerge(Merge3.java:114)
at CIRI_Full2.main(CIRI_Full2.java:280)

FYI: the folder CIRI_output is empty as well, while the folder CIRI-full_output contains 4 files inside:
CIRI_output_ro1_align.txt CIRI_output_ro1.fq CIRI_output_ro2_info.list CIRI_output_ro2.sam

Thank you for your help.

Best,
Simone