Exception

[QuinLan-SWU]

Hello,Prof.Li.There was one exception when i run the tool.The details are as follows: Exception in thread "main" java.lang.ClassCastException: A REGION object expected. at LGL.data.REGION.compareTo(REGION.java:86) at LGL.data.CLUSTER.sortHeadTail(CLUSTER.java:150) at LGL.data.CLUSTER.(CLUSTER.java:102) at process.Pet2Cluster1.preCluster(Pet2Cluster1.java:64) at process.InteractionCalling.run(InteractionCalling.java:26) at process.Main.main(Main.java:104)

This means that the program stopped at Step5: Interaction Calling and just like follows:

[Mon Oct 21 10:54:53 CST 2019] Step4: Categorization of PETs ... [Mon Oct 21 10:54:53 CST 2019] start PetClassification ... [Mon Oct 21 10:54:53 CST 2019] start loading PETs from /public/home/yhsun/DRN/Hi-C/test/result/result.bedpe.selected.pet.txt [Mon Oct 21 10:54:53 CST 2019] 0.554681M PETs read from /public/home/yhsun/DRN/Hi-C/test/result/result.bedpe.selected.pet.txt [Mon Oct 21 10:54:53 CST 2019] Step5: Interaction Calling ... PS: Read file for stderr output of this job.

The command line:

java -jar /public/home/yhsun/opt/biosoft/ChIA-PET_Tool_V3-master/ChIA-PET.jar --mode 1 --fastq1 test_R1.fq --fastq2 test_R2.fq --linker ./linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /public/home/yhsun/genome/maizeversion36/maize36.fa --GENOME_LENGTH 2.2e9 --CHROM_SIZE_INFO /public/home/yhsun/genome/genomechro/genome_size_2.txt --CYTOBAND_DATA ./chromInfo/maize_cytoBandIdeo.txt --SPECIES 3 --output /public/home/yhsun/DRN/Hi-C/test --prefix result --thread 4

[ValdemarP267]

Hi, I am experiencing the same issue [Fri Apr 03 17:15:06 CEST 2020] Step5: Interaction Calling ... Exception in thread "main" java.lang.ClassCastException: A REGION object expected. at LGL.data.REGION.compareTo(REGION.java:86) at LGL.data.CLUSTER.sortHeadTail(CLUSTER.java:150) at LGL.data.CLUSTER.(CLUSTER.java:102) at process.Pet2Cluster1.preCluster(Pet2Cluster1.java:64) at process.InteractionCalling.run(InteractionCalling.java:26) at process.Main.main(Main.java:104)

The command line I run:

java -jar /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 0 --fastq1 /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short_1.fastq --fastq2 /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short_2.fastq --linker /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/linker/linker.txt --minimum_linker_alignment_score 8 --GENOME_INDEX /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/GENOME_INDEX/hg19.fa --GENOME_LENGTH 3E9 --CHROM_SIZE_INFO /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/hg19.chromSize.txt --CYTOBAND_DATA /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/hg19_cytoBandIdeo.txt --SPECIES 1 --output /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short --prefix K562 --thread 4

Since this post is few months old has it been resolved?

[GuoliangLi-HZAU]

Hi,

We don't think this is a software problem. From the error message, seems that the format of the data set is different from what expected. Please check the data set format.

Best regards, Guoliang

----------------Dr. Guoliang Li College of Informatics, Huazhong Agricultural University 1 Shizishan Jie, Hongshan Qu, Wuhan 430070, China Tel: 0086-27-87285078 email: guoliang.li@mail.hzau.edu.cn URL: http://www.guolianglab.org/

李国亮，博士 武汉市洪山区狮子山街1号 华中农业大学信息学院 邮编：430070 电话：027-87285078 实验室网站：http://www.guolianglab.org/

---------- Origin message ----------

From："ValdemarP267" notifications@github.com To："GuoliangLi-HZAU/ChIA-PET_Tool_V3" ChIA-PET_Tool_V3@noreply.github.com Subject：Re: [GuoliangLi-HZAU/ChIA-PET_Tool_V3] Exception (#2) Date：2020-04-03 23:27:24Hi, I am experiencing the same issue [Fri Apr 03 17:15:06 CEST 2020] Step5: Interaction Calling ... Exception in thread "main" java.lang.ClassCastException: A REGION object expected. at LGL.data.REGION.compareTo(REGION.java:86) at LGL.data.CLUSTER.sortHeadTail(CLUSTER.java:150) at LGL.data.CLUSTER.(CLUSTER.java:102) at process.Pet2Cluster1.preCluster(Pet2Cluster1.java:64) at process.InteractionCalling.run(InteractionCalling.java:26) at process.Main.main(Main.java:104)

The command line I run:

java -jar /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 0 --fastq1 /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short_1.fastq --fastq2 /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short_2.fastq --linker /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/linker/linker.txt --minimum_linker_alignment_score 8 --GENOME_INDEX /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/GENOME_INDEX/hg19.fa --GENOME_LENGTH 3E9 --CHROM_SIZE_INFO /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/hg19.chromSize.txt --CYTOBAND_DATA /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/hg19_cytoBandIdeo.txt --SPECIES 1 --output /mnt/z/Dropbox/Valdemar_WORK/ChIA-PET/ChIA-PET_Tool_V3/test_short --prefix K562 --thread 4

Since this post is few months old has it been resolved?

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3/issues/2#issuecomment-608505590

[ttian627]

I have the same problem with ValdemarP267. I used the test short read file downloaded form NCBI and the other files were provided by the ChIA-PET_Tool_V3. Could you help us to resolve it ?

[hcph]

It's all about the 'CHROM_SIZE_INFO' file, the chromosome name in this file should be the same with the 'ipet' file, and use 'chr' not 'Chr'. When I do like this, the problem fixed.

[abhiag2018]

It's all about the 'CHROM_SIZE_INFO' file, the chromosome name in this file should be the same with the 'ipet' file, and use 'chr' not 'Chr'. When I do like this, the problem fixed.

@HeChao7021 thanks. Download the new hg19.chromSize.txt from UCSC worked for me on the test short-read data provided above.