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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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Java error when running java -jar /apps/ciri/2.1.1/bin/CIRI_Full_v2.1.1.jar Pipeline #34

Open SimoneRossi94 opened 3 months ago

SimoneRossi94 commented 3 months ago

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