question about running CIRI-full

question about running CIRI-full


I’m using ciri-full to calculate the full length sequence of circRNAs ,and I can run the test data set successfully, but I can’t run my own data

running test data set:

java -jar ../CIRI-full.jar Pipeline -1 test_1.fq.gz -2 test_2.fq.gz -a test_anno.gtf -r test_ref.fa -d test_output/ -o test

and i get no error :

CIRI-full pipeline completed. Time used: 75s. Output file is under dir: ***/test_output/

running my data:

java -jar ../CIRI-full.jar Pipeline -1 ***_1.fastq.gz -2 ***_2.fastq.gz  -r  hg38.fa -d test_output/ -o test  -t 30

error appear:
error image1

it seems an ciri-as error ,so i ran ciri-as separately, and then use CIRI-full.jar Merge module:

java -jar ../../CIRI-full.jar Merge -c ../../test/test_output/test.ciri -as ../../test/test_output2/test_jav.list -ro ./CIRI-full_output/test_ro2_info.list -r ../hg38.fa -o merge

but there is an new error :
error image2

What`s the problem?



Source link