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GuoliangLi-HZAU / ChIA-PET_Tool_V3

ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization
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Exception in thread "main" java.lang.NullPointerException #3

Open Qi-Yang-Bioinfo opened 3 years ago

Qi-Yang-Bioinfo commented 3 years ago

Hi Guoliang , I ran into a java exception on sample data test_long, can you offer some help, please?

My command line: java -jar ChIA-PET.jar --mode 1 --fastq1 test_long_1.fastq --fastq2 test_long_2.fastq --linker linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX ./bwa_index_GRCh38/GRCh38 --GENOME_LENGTH 3E9 --CHROM_SIZE_INFO chrom_GRCh38.sizes --CYTOBAND_DATA ./ref/cytoBandIdeo.txt --SPECIES 1 --output /./Results --prefix test_long --thread 16

the screen output: [Sun Oct 11 17:52:35 CST 2020] start ChIA-PET analysis [Sun Oct 11 17:52:35 CST 2020] Step1: Linker filtering ... [Sun Oct 11 17:53:14 CST 2020] Step2: Mapping to genome ... [Sun Oct 11 17:55:22 CST 2020] Step3: Removing redundancy ... [Sun Oct 11 17:55:48 CST 2020] start MergeSimilarPETs2 ... number of pets = 45801 [Sun Oct 11 17:55:49 CST 2020] start MergeSimilarPETs2 ... number of pets = 17172 [Sun Oct 11 17:55:51 CST 2020] start MergeSimilarPETs2 ... number of pets = 33520 [Sun Oct 11 17:55:52 CST 2020] start MergeSimilarPETs2 ... number of pets = 14786 [Sun Oct 11 17:55:54 CST 2020] start MergeSimilarPETs2 ... number of pets = 25430 [Sun Oct 11 17:55:56 CST 2020] start MergeSimilarPETs2 ... number of pets = 27858 [Sun Oct 11 17:55:56 CST 2020] start MergeSimilarPETs2 ... number of pets = 5762 [Sun Oct 11 17:55:58 CST 2020] start MergeSimilarPETs2 ... number of pets = 25540 [Sun Oct 11 17:56:01 CST 2020] start MergeSimilarPETs2 ... number of pets = 41711 [Sun Oct 11 17:56:02 CST 2020] start MergeSimilarPETs2 ... number of pets = 6535 [Sun Oct 11 17:56:02 CST 2020] start MergeSimilarPETs2 ... number of pets = 8609 [Sun Oct 11 17:56:03 CST 2020] start MergeSimilarPETs2 ... number of pets = 8231 [Sun Oct 11 17:56:04 CST 2020] start MergeSimilarPETs2 ... number of pets = 13560 [Sun Oct 11 17:56:05 CST 2020] start MergeSimilarPETs2 ... number of pets = 9343 [Sun Oct 11 17:56:05 CST 2020] start MergeSimilarPETs2 ... number of pets = 5210 [Sun Oct 11 17:56:05 CST 2020] start MergeSimilarPETs2 ... number of pets = 2766 [Sun Oct 11 17:56:06 CST 2020] start MergeSimilarPETs2 ... number of pets = 15855 [Sun Oct 11 17:56:08 CST 2020] start MergeSimilarPETs2 ... number of pets = 15075 [Sun Oct 11 17:56:10 CST 2020] start MergeSimilarPETs2 ... number of pets = 19697 [Sun Oct 11 17:56:10 CST 2020] start MergeSimilarPETs2 ... number of pets = 7490 [Sun Oct 11 17:56:11 CST 2020] start MergeSimilarPETs2 ... number of pets = 7025 [Sun Oct 11 17:56:11 CST 2020] start MergeSimilarPETs2 ... number of pets = 1878 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 4720 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 197 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 3 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 2 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 2 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 3 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 6 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 6 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 2 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 2 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:12 CST 2020] start MergeSimilarPETs2 ... number of pets = 1 [Sun Oct 11 17:56:20 CST 2020] Step4: Categorization of PETs ... [Sun Oct 11 17:56:20 CST 2020] start PetClassification ... [Sun Oct 11 17:56:20 CST 2020] start loading PETs from /media/oxygen/disk1/YangQi/1.ChIA-PET-project/Results/test_long/test_long.bedpe.selected.pet.txt [Sun Oct 11 17:56:21 CST 2020] 0.363767M PETs read from /media/oxygen/disk1/YangQi/1.ChIA-PET-project/Results/test_long/test_long.bedpe.selected.pet.txt [Sun Oct 11 17:56:21 CST 2020] Step5: Interaction Calling ... Exception in thread "main" java.lang.NullPointerException 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)

Qi-Yang-Bioinfo commented 3 years ago

update: I got the same error on test_short dataset.

update2: tried different jdk version(14, 11, 8), all got the same error

hahaha12379 commented 1 year ago

Hi, I'm having the same problem as you. Can you tell me how you solved it later?Thank you very much!

hcph commented 1 year ago

The genome_table you provided may have some problems, you can check whether the chromosome ID is consistent with fasta file, and whether it contains all the chromosome s-------- 原始邮件 --------发件人： Cecilia @.>日期： 2022年12月28日周三 晚上8:58收件人： GuoliangLi-HZAU/ChIA-PET_Tool_V3 @.>抄送： HC @.>, Comment @.>主 题： Re: [GuoliangLi-HZAU/ChIA-PET_Tool_V3] Exception in thread "main" java.lang.NullPointerException (#3) Hi, I'm having the same problem as you. Can you tell me how you solved it later?Thank you very much!

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