CIRI-vis fails to generate a fasta file

[drwazeem]

I analyzed 12 sets of paired end reads with CIRI-full pipeline and tried to run CIRI-vis on each of them. 11 samples worked fine but for the 12th sample, CIRI-vis generates the circRNA plots and list file, but doesn't output the fasta file. In the Terminal, following error is produced:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:266) at java.base/java.util.Objects.checkIndex(Objects.java:359) at java.base/java.util.ArrayList.get(ArrayList.java:427) at sample_MIX_all_easy4.paint(sample_MIX_all_easy4.java:1278) at CIRI_vis_test.main(CIRI_vis_test.java:457)

Command used:
java -Xmx4096m -jar CIRI-vis_v1.4.jar -i sampleX_merge_circRNA_detail.anno -l sampleX.as_library_length.list -r genome.fa -min 1 -d sampleX/ciri_vis_out -o sampleX

TL,DR:
**CIRI-vis generates:
PDFs of detected circRNAs
.list file

CIRI doesn't generate:
list_circle.fa file**

[Alipe2021]

I got the same error. The .list file is empty.

[Kevinzjy]

Hi @drwazeem , could you try the latest version of CIRI-vis from https://github.com/bioinfo-biols/CIRI-vis ? The executable jar file is located under the bin directory.

[drwazeem]

@Kevinzjy Again the same problem. Output is given below:
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at sample_MIX_all_easy4.paint(sample_MIX_all_easy4.java:1275) at CIRI_vis_test.main(CIRI_vis_test.java:437)

Another point I wanted to add: CIRI-viz works fine if I use CIRI_AS output (.jav_list; -d yes) for all samples, including this one.

[Kevinzjy]

@Kevinzjy Again the same problem. Output is given below: Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at sample_MIX_all_easy4.paint(sample_MIX_all_easy4.java:1275) at CIRI_vis_test.main(CIRI_vis_test.java:437)

Another point I wanted to add: CIRI-viz works fine if I use CIRI_AS output (.jav_list; -d yes) for all samples, including this one.

Yes, '-d yes' is required if you run CIRI2/CIRI-AS/CIRI-full manually. You could refer to the section the following section (https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#how-to-run-the-test-data-set-using-ciri-full) for the full commands.

[drwazeem]

Yep that works well without any problems.
I am facing problems with just one sample when using the below command:

java -Xmx4096m -jar CIRI-vis_v1.4.jar -i sampleX_merge_circRNA_detail.anno -l sampleX.as_library_length.list -r genome.fa -min 1 -d sampleX/ciri_vis_out -o sampleX
Or

java -Xmx4096m -jar CIRI-vis_v1.4.1.jar -i sampleX_merge_circRNA_detail.anno -l sampleX.as_library_length.list -r genome.fa -min 1 -d sampleX/ciri_vis_out -o sampleX

[Alipe2021]

Again the same problem. Output is given below:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
        at java.base/java.util.Objects.checkIndex(Objects.java:372)
        at java.base/java.util.ArrayList.get(ArrayList.java:459)
        at sample_MIX_all_easy4.paint(sample_MIX_all_easy4.java:1275)
        at CIRI_vis_test.main(CIRI_vis_test.java:437)

In the previous CIRI-AS step, I had added the param -D yes.

[Kevinzjy]

Hi @drwazeem @Alipe2021 , we've updated a fixed commit at bioinfo-biols/CIRI-vis@bfbffe0, could you please try it again?

[drwazeem]

@Kevinzjy I have tried both. This thread strarted with CIRI-vis_v1.4.jar, but as I said there is the same issue with CIRI-vis_v1.4.1.jar.

Both of them work well when CIRI_as output is used; but both of them fail to generate the fasta file to process one of my 12 samples when I directly use CIRI-full (merge_circRNA_detail.anno) output.

[Alipe2021]

Consistent with previous problem,

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
        at java.base/java.util.Objects.checkIndex(Objects.java:372)
        at java.base/java.util.ArrayList.get(ArrayList.java:459)
        at sample_MIX_all_easy4.paint(sample_MIX_all_easy4.java:1275)
        at CIRI_vis_test.main(CIRI_vis_test.java:431)