bioinfo-biols / ciri-cookbook Goto Github PK

Command I am using : java -jar CIRI_Full_v2.1.1.jar Merge -c 759_prefix_CIRI -as 759_Raw_Prefix_CIRI_AS_jav.list -ro 759_RO2_ro2_info.list -a genomic.gtf -r GCF_002263795.2_ARS-UCD1.3_genomic.fna -o 759_Merge

classpath = /
Output prefix = /media/firu/TOSHIBA/CIRI/759_Merge

Merge module start

Loading Annotation...
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 2 out of bounds for length 1
at Merge3.getmerge(Merge3.java:77)
at CIRI_Full2.main(CIRI_Full2.java:555)

The java version that I am using is below:
java version "19.0.1" 2022-10-18
Java(TM) SE Runtime Environment (build 19.0.1+10-21)
Java HotSpot(TM) 64-Bit Server VM (build 19.0.1+10-21, mixed mode, sharing)

Can anyone please help.

Hello! Thanks for making this interesting tool. I am trying to install ciri2 on a cluster but I am struggling.

I am following the CIRI cookbook https://ciri-cookbook.readthedocs.io/_/downloads/en/latest/pdf/.

I have found and (seemingly) installed CIRI_v2.0.6.zip, however this is not sufficient to run the full pipeline.

To use CIRI-full.jar, the cookbook directs me to download and unzip CIRI-full.zip. I have not been able to find CIRI-full.zip, only CIRI_Full_v2.1.1.jar (from https://sourceforge.net/projects/ciri/files/CIRI-full/CIRI_Full_v2.1.1.jar/download). I tried to unzip this instead, as follows;

#!/bin/bash
module load Perl/5.34.0-GCCcore-11.2.0
module load Python/3.9.6-GCCcore-11.2.0
module load BWA/0.7.17-GCCcore-11.2.0
unzip CIRI_Full_v2.1.1.jar
module purge

This produced a bunch of files and directories;
replace .project? [y]es, [n]o, [A]ll, [N]one, [r]ename:
inflating: reversc.java
inflating: Exon_cov2.java
inflating: Exon_gtf.java
inflating: sam5.java
inflating: index_head_finder2.java
inflating: RO2.java
inflating: index_head_finder_more.java
inflating: Merge3.java
inflating: CIRI_Full2.java
inflating: Seq.java
inflating: Exon_length.java
inflating: RO1_single.java
inflating: CIRI_Full2$1.class
inflating: CIRI_Full2$2.class
inflating: CIRI_Full2$3.class
inflating: CIRI_Full2$4.class
inflating: CIRI_Full2.class
inflating: Exon_cov2.class
inflating: Exon_gtf.class
inflating: Exon_length.class
inflating: Merge3.class
inflating: RO1_single.class
inflating: RO2.class
inflating: Seq.class
inflating: index_head_finder2.class
inflating: index_head_finder_more.class
inflating: reversc.class
inflating: sam5.class

However, trying to run CIRI_FULL2.java using the cookbook code produces the following error:
$ java -jar CIRI_Full_v2.1.1.jar
Error occurred during initialization of VM
Could not allocate metaspace: 1073741824 bytes

Overall, I am unclear on how to install your tool and the cookbook isn't helping. Please provide some guidance.
Thanks,
Dan

Hi guys,
I get the following error at the Merge step of the CIRI-full script:
Loading CIRI_AS output... Exception in thread "main" java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:567) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58) Caused by: java.io.FileNotFoundException: /hpctmp/phaei/GSE/CIRI_full/./CIRI_full_out/SRR/CIRI-AS_output/SRR_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:213) at java.base/java.io.FileInputStream.<init>(FileInputStream.java:155) at java.base/java.io.FileInputStream.<init>(FileInputStream.java:110) at java.base/java.io.FileReader.<init>(FileReader.java:60) at Merge3.getmerge(Merge3.java:114) at CIRI_Full2.main(CIRI_Full2.java:280)

It seems to be unable to find the prefix_jav.list file. The previous step of RO2 runs fine with no errors but the output folder CIRI-AS_output is completely empty.
Any help would be greatly appreciated

I know CIRI2 will filter reads by PEM signals. But i am confused about if the inner distance of ciricular RNA reads is low, will CIRI2 filter this reads by PEM signals.

Hi guys,

I got an new error when running the command: java -jar /opt/biosoft/CIRI-full_v2.0/CIRI-vis_v1.4.jar -i out_merge_circRNA_detail.anno -l output_library_length.list -r zma_dna_v4.fa -min 1 -d test_outdir -o circRNA . I donot fix it. Can any one help me.

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:1278)
        at CIRI_vis_test.main(CIRI_vis_test.java:457)

OS: opensuse 15.2
Java version:

CIRI-vis 1.4

Hi all,
When I run CIRIquant, I am able to run CIRIquant to completion but have not been able to get out anything in the gene folder. The .log says "Error: no valid ID found for GFF record" which is weird since the manual doesn't ask for a GFF file. When I use a GFF file instead of a GTF file, I am able to get a gene abundance score but the program will no longer run to completion. I need the gene abundance scores for DE (with biological replicates). Is there something that I might be doing wrong to get this error?
A

Dear Sir,

Is there any way to merge the .ciri from several samples generated by CIRI2?

Here is another issue. Can CIRIquant use raw fastq file as input? As CIRI_AS could not use sam files generated from trimmed fastq file. We uased raw fastq file for bwa alignment and CIRI2.

Thanks.

Hi guys,

When I run CIRIquant, /home/justin/miniconda2/bin/CIRIquant -t 15 \ -1 /home/biodata/GSE135055/2.clean/SRR9856187_1_val_1.fq.gz \ -2 /home/biodata/GSE135055/2.clean/SRR9856187_2_val_2.fq.gz \ --config /home/biodata/GSE135055_CIRCRNA/chr1.yml \ -o /home/biodata/GSE135055_CIRCRNA/SRR9856187 \ -p SRR9856187 >CIRIquant_SRR9856187.test.log
I'm stuck at a certain step as follows:

Total time for call to driver() for forward index: 00:01:49
[Fri 2022-04-22 15:38:15] [INFO ] De novo alignment for circular RNAs ..
48182911 reads; of these:
48182911 (100.00%) were paired; of these:
44344044 (92.03%) aligned concordantly 0 times
1045458 (2.17%) aligned concordantly exactly 1 time
2793409 (5.80%) aligned concordantly >1 times
----
44344044 pairs aligned concordantly 0 times; of these:
13208 (0.03%) aligned discordantly 1 time
----
44330836 pairs aligned 0 times concordantly or discordantly; of these:
88661672 mates make up the pairs; of these:
85158214 (96.05%) aligned 0 times
1041907 (1.18%) aligned exactly 1 time
2461551 (2.78%) aligned >1 times
11.63% overall alignment rate
[bam_sort_core] merging from 30 files and 15 in-memory blocks...
[Fri 2022-04-22 16:24:29] [INFO ] Detecting reads containing Back-splicing signals
[Fri 2022-04-22 16:24:59] [INFO ] Detecting FSJ reads from genome alignment file

Bed files are generated, but GTF quantitative files are not generated. No error message is reported. The specific log file is in the attachment.

Can any one help me to solve this problem. Thanks
SRR9856187.log
.

Hello，can CIRIquant be used to analyse the single end data? CIRI2 can analyse single or paired end data,but when i want to do differential expression of cir-RNA using CIRIquant, I find the CIRIquant just can be input paired data because of the " -1 -2 "parameter, so can you test me how to deal with it, or should i use other tools? For example, the other tools "sailfish-as‘’ can be
used for single or paired data，because its parameter " -1 -2 for paried end data (.fastq.gz) , and -r for single end data(.fastq.gz), but i don't find it in CIRIquant parameter.
THANKS

Hi guys,
I am using CIRI-full_v2.0 with updated java version. CIRI-full pipeline worked well but when I used CIRI-vis.jar with the following command it showed error message.
$ java -jar ../CIRI-vis.jar -i circ_output/prefix_merge_circRNA_detail.anno -l circ_output/prefix_library_length.list -r hg38.fa -d CIRI-vis/ -min 1

"Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2D
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:398)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)
Caused by: java.lang.ClassNotFoundException: org.apache.batik.svggen.SVGGraphics2D
at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:471)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:589)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 3 more
"

I checked my java version using
$java -version

openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)

Please help.

Hi guys,
I get the following error when I try to run the Merge module.

Merge module start

Loading Annotation...
Annotation Loaded
Loading CIRI_AS output...
CIRI_AS output Loaded
Loading CIRI output...
CIRI output Loaded
Loading CIRI_RO output...
CIRI_RO output Loaded
Combine AS and RO output
Combine completed, 71 reads are used
Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:483)
        at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
        at Exon_gtf.get_exon(Exon_gtf.java:16)
        at Merge3.getmerge(Merge3.java:784)
        at CIRI_Full2.main(CIRI_Full2.java:551)
        ... 5 more

I have all the outputs of CIRI, prefix_jav.list and prefix_ro2_info.list. The logs are empty not errors are shown.
Hope to get a response soon.
regards

Hi there,
I'd like to try using CIRI2 or CIRIquant to map circRNA reads in human genome. But since my project has over 1000 samples and we've already done the alignment work for mRNA by STAR aligner (which took lots of time), so I just wonder whether these tools may allow for the STAR-generated BAM file as a input? Because if we rerun the genome alignment pipeline using bwa-mem once again, that could cost a lot of time..
Thanks a lot and looking forward to your kind reply!
Best regards,
Weiqian Jiang

I am running into an issue running the merge function. It appears to be working but then failing during the creation of the output file. Below is the log file. I'm unsure what may be going wrong and haven't had any issues with the other steps of CIRI-full.
Thank you,
A

classpath = bin/
Output prefix = /panfs/jay/groups/5/reedkm/shared/CIRI2/Powell_Prj015/test/sample12_merge

Merge module start

Loading Annotation...
Annotation Loaded
Loading CIRI_AS output...
CIRI_AS output Loaded
Loading CIRI output...
CIRI output Loaded
Loading CIRI_RO output...
CIRI_RO output Loaded
Combine AS and RO output
Combine completed, 13 reads are used
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
at Exon_gtf.get_exon(Exon_gtf.java:16)
at Merge3.getmerge(Merge3.java:770)
at CIRI_Full2.main(CIRI_Full2.java:551)
... 5 more

Once the user identifies differentially expressed circRNA, how can the miRNA they interact with be predicted? The IDs given to the transcripts by CIRIquant are not in some standard format such as circBase or circAtlas accept. It would be great to see a chapter in Cookbook about it.

Hi thank you for developing this cool tool!
I am using CIRIquant from fastq with following command.
CIRIquant -t 30 \ -1 $read_1 \ -2 $read_2 \ --config $BASE/CIRIquant.config \ -o $BASE/CIRI_quant_output \ -p $SAMPLE
When CIRI2 started, I have got an error like below.

SAM was divided successfully.

 First read of divided SAM files: 
SAMPLE1_unmapped.sambc: @PG
SAMPLE1_unmapped.sambd: @PG
Fail to record first reads for 30 pieces of SAM.
Fatal error. Aborted.

Looking to the divided SAMs, they were split in the middle of a line like below.
@SQ SN:chrUn_

Would you please give any suggestion to solve this?
Thanks.

The example shown in CIRI_DE -n control.gtf -c case.gtf -o CIRI_DE.csv. But, the output file is actually a tab-separated text file. What about showing txt or tsv instead of csv for -o?

As the title, I had suffered from this.

I get this error message when I run CIRI_Full_v2.1.1.jar Pipeline .

Exception in thread "main" java.io.FileNotFoundException: RNASeq_LacZAZA_D5_2_CIRI/CIRI-AS_output/RNASeq_LacZAZA_D5_2_CIRI_jav.list (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at Merge3.getmerge(Merge3.java:114)
at CIRI_Full2.main(CIRI_Full2.java:280)

I checked CIRI-AS_output folder and not files are generated there.

Hello everyone,

I downloaded 5 TCGA-BRCA samples (by choosing specific criteria - I got five tumor samples and their five normal samples) and I run CIRIquant on them. I performed differential expression analysis using CIRI_DE_replicate and I got the final table. My question is: Do you have any idea why would I get good log2 fold change values but not statistically significant (all FDR values are greater than 0.05)?

I appreciate your advice and thanks in advance.

Hello there,
Thanks a lot for this package! I just have a question about the differential expression analysis, just to make sure I am reading the output in the correct way: when we say differential expression here, the results shown are for case vs control and not for control vs case, right?

Thanks in advance.

Hi all,
I was wondering if it is possible to run CIRI-full on single-end reads? the Docs only show examples for paired-end.

regards

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**

trying to run CIRI-AS after running both CIRIv1 and CIRI2 and I am encountering different issues for both.
When running CIRIv1 I get the following error:
Please make sure all the reads have the same read lengths!
When running CIRI2 I get error that everyone else gets:
"Please make sure the SAM is the same one used for circRNA detection by CIRI without modification!"

I used the same SAM file for all. I was also wondering if it is a good idea to use raw fastq files (NO adapter trimming) with CIRI. Does that affect the results?

Hi guys,

When I ran the command:

CIRIquant --config circ_quant_cfg.yaml -1 sampleA.R1.fq.gz -2 sampleA.R2.fq.gz --bam sampleA_sorted.bam  -o ./sampleA -p sampleA  -t 8 --bed CircRNAs.bed -e CIRIquant.log

It got an error as follows:

[Wed 2022-03-02 20:34:12] [INFO ] Detecting FSJ reads from genome alignment file
Traceback (most recent call last):
  File "/opt/miniconda3/envs/CIRIquant_env/bin/CIRIquant", line 11, in <module>
    load_entry_point('CIRIquant==1.1.2', 'console_scripts', 'CIRIquant')()
  File "/opt/miniconda3/envs/CIRIquant_env/lib/python2.7/site-packages/CIRIquant-1.1.2-py2.7.egg/CIRIquant/main.py", line 184, in main
    out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type)
  File "/opt/miniconda3/envs/CIRIquant_env/lib/python2.7/site-packages/CIRIquant-1.1.2-py2.7.egg/CIRIquant/circ.py", line 656, in proc
    bsj_reads, fsj_reads = proc_genome_bam(hisat_bam, thread, circ_info, cand_bsj, anchor, circ_dir)
  File "/opt/miniconda3/envs/CIRIquant_env/lib/python2.7/site-packages/CIRIquant-1.1.2-py2.7.egg/CIRIquant/circ.py", line 434, in proc_genome_bam
    tmp = job.get()
  File "/opt/miniconda3/envs/CIRIquant_env/lib/python2.7/multiprocessing/pool.py", line 572, in get
    raise self._value
ValueError: start out of range (-1)

Can any one help me to solve this problem. Thanks.

I did run CIRIquant with command:
CIRIquant -t 20 -1 /data/circRNA_fastq_files/2_S2_L001_R1_001.fastq.gz -2 /data/circRNA_fastq_files/2_S2_L001_R2_001.fastq.gz --config /dmel_ENS_BDGP6_myCIRIquant.yml -p 2_S2 --library-type 1 and I get the following error:
[Wed 2022-06-08 12:44:20] [INFO ] Input reads: 2_S2_L001_R1_001.fastq.gz,2_S2_L001_R2_001.fastq.gz
[Wed 2022-06-08 12:44:20] [INFO ] Library type: ScriptSeq
[Wed 2022-06-08 12:44:20] [INFO ] Output directory: /home/ml98b/2_S2, Output prefix: 2_S2
[Wed 2022-06-08 12:44:20] [INFO ] Config: dmel_ENS_BDGP6 Loaded
[Wed 2022-06-08 12:44:20] [INFO ] 40 CPU cores availble, using 20
[Wed 2022-06-08 12:44:20] [INFO ] Align RNA-seq reads to reference genome ..
Traceback (most recent call last):
File "/home/ml98b/.conda/envs/CIRI/bin/CIRIquant", line 8, in
sys.exit(main())
File "/home/ml98b/.conda/envs/CIRI/lib/python2.7/site-packages/CIRIquant/main.py", line 152, in main
hisat_bam = pipeline.align_genome(log_file, thread, reads, outdir, prefix)
File "/home/ml98b/.conda/envs/CIRI/lib/python2.7/site-packages/CIRIquant/pipeline.py", line 51, in align_genome
if os.path.getsize(sorted_bam + '.bai') <= 16:
File "/home/ml98b/.conda/envs/CIRI/lib/python2.7/genericpath.py", line 57, in getsize
return os.stat(filename).st_size
and the logFile out is:
[Wed 2022-06-08 12:44:20] [INFO ] Input reads: 2_S2_L001_R1_001.fastq.gz,2_S2_L001_R2_001.fastq.gz
[Wed 2022-06-08 12:44:20] [INFO ] Library type: ScriptSeq
[Wed 2022-06-08 12:44:20] [INFO ] Output directory: /home/ml98b/2_S2, Output prefix: 2_S2
[Wed 2022-06-08 12:44:20] [INFO ] Config: dmel_ENS_BDGP6 Loaded
[Wed 2022-06-08 12:44:20] [INFO ] 40 CPU cores availble, using 20
[Wed 2022-06-08 12:44:20] [INFO ] Align RNA-seq reads to reference genome ..
/home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5) /home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.17' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5)
/home/ml98b/.conda/envs/CIRI/bin/hisat2-align-s: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/libstdc++.so.6) /home/ml98b/.conda/envs/CIRI/bin/hisat2-align-s: /lib64/libc.so.6: version GLIBC_2.16' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/libstdc++.so.6)
/home/ml98b/.conda/envs/CIRI/bin/hisat2-align-s: /lib64/libc.so.6: version GLIBC_2.17' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/libstdc++.so.6) /home/ml98b/.conda/envs/CIRI/bin/hisat2-align-s: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/libgcc_s.so.1)
(ERR): Description of arguments failed!
Exiting now ...
/home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5) /home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.17' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5)
/home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5) /home/ml98b/.conda/envs/CIRI/bin/samtools: /lib64/libc.so.6: version GLIBC_2.17' not found (required by /home/ml98b/.conda/envs/CIRI/bin/../lib/./liblzma.so.5)

My memory is 256GB ; however, I got the following message:
[Tue 2022-06-21 07:11:12] [INFO ] Input reads: SRR9856190_1_val_1.fq.gz,SRR9856190_2_val_2.fq.gz
[Tue 2022-06-21 07:11:12] [INFO ] Library type: unstranded
[Tue 2022-06-21 07:11:12] [INFO ] Output directory: /home/biodata/GSE135055_CIRCRNA/SRR9856190_out, Output prefix: SRR9856190
[Tue 2022-06-21 07:11:12] [INFO ] Config: GRCh38 Loaded
[Tue 2022-06-21 07:11:12] [INFO ] 40 CPU cores availble, using 35
[Tue 2022-06-21 07:11:12] [INFO ] Align RNA-seq reads to reference genome ..
[Tue 2022-06-21 08:02:43] [INFO ] Estimate gene abundance ..
[Tue 2022-06-21 08:11:28] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction ..
[Tue 2022-06-21 08:11:28] [INFO ] Running BWA-mem mapping candidate reads ..
[Tue 2022-06-21 08:24:53] [INFO ] Running CIRI2 for circRNA detection ..
[Tue 2022-06-21 09:10:32] [INFO ] Extract circular sequence
[Tue 2022-06-21 09:10:55] [100% ] [##################################################]
[Tue 2022-06-21 09:10:55] [INFO ] Building circular index ..
[Tue 2022-06-21 09:12:55] [INFO ] De novo alignment for circular RNAs ..
[Tue 2022-06-21 09:56:22] [INFO ] Detecting reads containing Back-splicing signals
[Tue 2022-06-21 09:56:56] [INFO ] Detecting FSJ reads from genome alignment file
Traceback (most recent call last):
File "/home/justin/miniconda2/bin/CIRIquant", line 10, in
sys.exit(main())
File "/home/justin/miniconda2/lib/python2.7/site-packages/CIRIquant/main.py", line 183, in main
out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type)
File "/home/justin/miniconda2/lib/python2.7/site-packages/CIRIquant/circ.py", line 656, in proc
bsj_reads, fsj_reads = proc_genome_bam(hisat_bam, thread, circ_info, cand_bsj, anchor, circ_dir)
File "/home/justin/miniconda2/lib/python2.7/site-packages/CIRIquant/circ.py", line 434, in proc_genome_bam
tmp = job.get()
File "/home/justin/miniconda2/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
MemoryError

How can I sovle this problem?

Hello,

I'm not having any problems running the CIRI-full module up until the RO2 module. At that point, I'm getting this exception:

Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.StringIndexOutOfBoundsException: begin 0, end 1, length 0
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3319)
at java.base/java.lang.String.substring(String.java:1874)
at RO2.getro2(RO2.java:238)

Any ideas?

Hi guys,
I am encountering a new error when running CIRI_vis
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2D at java.base/java.lang.Class.forName0(Native Method) at java.base/java.lang.Class.forName(Class.java:416) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56) Caused by: java.lang.ClassNotFoundException: org.apache.batik.svggen.SVGGraphics2D at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:436) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:588) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521) ... 3 more

Running on centos. Hope I can get some help. I am not familiar with JAVA at all.

regards