problem in running CIRI2 as a circular RNA extracting tool

Question

[modarzi]

hi,

I read this artile: "CIRI: an efficient and unbiased algorithm for de novo circular RNA identification." CIRI is a tool for extracting circular RNA. so, I downloaded CIRI2 and for running this tool based on test_data I execute below command:

perl CIRI2.pl -I test.sam -O outfile -F chr1.fa -A chr1.gtf

but I see below error:

the following chromosomes are not founds in chr1.fa: chr 16 chr6 chr17 chr 19 chr 7 chr 8 chr 2 chr 10 chr 9 chr 18 chr 20 chr 12 chr 11 chr 15 chr X chr 13 chrY chr21 chr14 chr3 chr4 chr22
Fatal error. Aborted.

I appreciate if anybody share his/her comment with me.

Best regards,

Mohammad

[WouterDeCoster]

Do the chromosome names match between the gtf and fa?

[modarzi]

Yes, my command is based on example of CIRI2_mamual.txt. I didn't any changing on the name of files and command.

[WouterDeCoster]

I see chromosomes with a space (e.g. chr 11) and without (e.g. chr4). Something is odd.

Do the chromosome names match between the gtf, the sam and the fa?

[modarzi]

exactly this is error:

The following chromosomes are not found in chr1.fa: chr3 chr16 chr22 chr11 chrY chr7 chr4 chr19 chr21 chr6 chr12 chr15 chr17 chr5 chr18 chr9 chrX chr2 chr10 chr20 chr14 chr13 chr8 Fatal error. Aborted.