#5 Error in running CIRI2

[Mohammad]

Dear Author of Article: CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.

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 appericite if anybody share his/her comment with me.
Best regards,
Mohammad

[Yuan Gao]

Hi Mohammad,
Please download test_data2.zip contained in the CIRI2 folder to test CIRI2.
Thanks,
Yuan

[Mohammad]

Hi Yuan

Thanks

Mohammad

[Md Golam Rbbani]

Hi Yuan,
I am using CIRI2 to analyse my data set using
Perl CIRI2 -I in.sam -O out.ciri -F reference.fa -A reference.gtf -T 4 command but getting error message
CIRI2 cannot understand reference.gtf. at CIRI.pl line 319, <anno> line 1.</anno>

DO i need to run without .gtf file in CIRI2??

Thanks
Rabbani

[Jinyang Zhang]

Hi Rabbani,
Please check the attribute column (column 9) in your reference.gtf. CIRI2 need the "gene_id" attribute for circRNA annotation. If your annotation file do not provide this information, you need to run CIRI2 without it.

[Md Golam Rbbani]

Hello Jinyang,
Reference GTF looks fine. it has "gene_id" attribute

[Jinyang Zhang]

Hi Rabbani,

I am not sure what cause the problem. If the first few lines of your GTF file contain header information start with '#', you can remove them and try again.

P.S. Are you using the latest version (v2.0.6) of CIRI2? It seems that the error message is generated from an obsolute version.

Thanks,

Jinyang

[Yuan Gao]

If you got the error message from line 319, that is due to the reference file (FASTA) cannot be found or read. I believe the error message is like "Reference file is not readable".

[Md Golam Rbbani]

Hi Yuan gao,
CIRI2 cannot understand reference.gtf. at CIRI.pl line 319, <anno> line
1.</anno>
This is the error message i have got in error long. According to Jinyang
Zhang's suggestion, i am using without GTF and it is working fine.
Could you please clarify it for me?

Thanks,
*Rabbani *

On Thu, Aug 29, 2019 at 6:55 PM Yuan Gao gy-james@users.sourceforge.net
wrote:

If you got the error message from line 319, that is due to the reference
file cannot be found or read. I believe the error message is like
"Reference file is not readable".

---

• [tickets:#5] https://sourceforge.net/p/ciri/tickets/5/ Error in
  running CIRI2*

Status: open
Milestone: 2.0
Labels: ERROR ciri2 chr1.fa
Created: Thu May 17, 2018 06:43 PM UTC by Mohammad
Last Updated: Wed Aug 28, 2019 11:56 AM UTC
Owner: nobody

Dear Author of Article: CIRI: an efficient and unbiased algorithm for de
novo circular RNA identification.

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 appericite if anybody share his/her comment with me.
Best regards,
Mohammad

---

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https://sourceforge.net/p/ciri/tickets/5/

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--

PhD fellow Md. Golam Rabbani

Genomics Research Group

Faculty of Biosciences and Aquaculture

Nord University

Universitetsalléen 11

8049 Bodø, Norway

Office 2125

[Yuan Gao]

Could you please send the first 100 lines of GTF file to me too (gy.james@163.com)? Thanks.

[Yuan Gao]

Hi Golam,
I think I know what the problem is. There are 420 lines in your GTF which do not have the key words “gene_id”. For example, "NC_035898.1 Gnomon exon 10221156 10221698 . - . transcript_id "id17563"; gene_name "LOC111194270”;". Please remove or modify these lines so that CIRI2 can run successfully.
Thanks,
Yuan

[Md Golam Rbbani]

Dear Yuan,
I want to ask you one more question. If i run ciri without gtf i win not
have information of circular rna type and gene id but will it predict
circular rna correctly?

Thanks
Rabbani

On Thu, Aug 29, 2019 at 11:20 PM Yuan Gao gy-james@users.sourceforge.net
wrote:

Hi Golam,
I think I know what the problem is. There are 420 lines in your GTF which
do not have the key words “gene_id”. For example, "NC_035898.1 Gnomon exon
10221156 10221698 . - . transcript_id "id17563"; gene_name
"LOC111194270”;". Please remove or modify these lines so that CIRI2 can run
successfully.
Thanks,
Yuan

---

• [tickets:#5] https://sourceforge.net/p/ciri/tickets/5/ Error in
  running CIRI2*

Status: open
Milestone: 2.0
Labels: ERROR ciri2 chr1.fa
Created: Thu May 17, 2018 06:43 PM UTC by Mohammad
Last Updated: Thu Aug 29, 2019 07:39 PM UTC
Owner: nobody

Dear Author of Article: CIRI: an efficient and unbiased algorithm for de
novo circular RNA identification.

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 appericite if anybody share his/her comment with me.
Best regards,
Mohammad

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/ciri/tickets/5/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

--

PhD fellow Md. Golam Rabbani

Genomics Research Group

Faculty of Biosciences and Aquaculture

Nord University

Universitetsalléen 11

8049 Bodø, Norway

Office 2125

[Yuan Gao]

As we mentioned in our paper and manual, CIRI is a de novo detection tool, which does not depend on annotation for detecting loci of circRNAs on reference genome and can be used for non-model organisms without complete annotation. The annotation can be used for output of gene ID for detected circRNAs or as a complementary filtration in addition to GT-AG splicing signals, but the detected circRNAs are almost the same whether annotation is provided or not.

[Md Golam Rbbani]

Hello JinYang,
I have tried V2.0.6 , v2.0.5 and v2.0.5. ALL of the virsion have same error message. HOwever, with CIRI1 it was fine. since i need strand info, i want to use CIRI2.

N.B : I have checked my GTF file and there is no header sequence that starts with '#' .

[Jinyang Zhang]

Hi Rabbani,
Sorry for the inconvenience. Could you send the GTF file or first 100 lines of it to my email zhangjinyang@biols.ac.cn ? I will check why CIRI2 failed to load your annotation file.

Thanks,

Jinyang

[Md Golam Rbbani]

Hello Jinyang,
I have send you the gtf file. Please check your email.

Thanks
Rabbani