Error in running. - Githubissues

I have something wrong in running, but I don't konw why. The information below: ` (ChIA-PET) sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker home/sun/anaconda3/envs/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output ChIA-PET_MH63 --prefix ChIA-PET --thread 20 Error: home/sun/anaconda3/envs/ChIA-PET_Tool_V3/linker/linker_long.txt doesn't exist (ChIA-PET) sun@sun-ubuntu:~$ less home/sun/anaconda3/envs/ChIA-PET_Tool_V3/linker/linker_long.txt home/sun/anaconda3/envs/ChIA-PET_Tool_V3/linker/linker_long.txt: 没有那个文件或目录 (ChIA-PET) sun@sun-ubuntu:~$ less /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt (ChIA-PET) sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output ChIA-PET_MH63 --prefix ChIA-PET --thread 20 Error: please check genome index (.amb, .ann, .bwt, pac and *.sa, these files are necessary) (ChIA-PET) sun@sun-ubuntu:~$ bwa index

Usage: bwa index [options]

Options: -a STR BWT construction algorithm: bwtsw, is or rb2 [auto] -p STR prefix of the index [same as fasta name] -b INT block size for the bwtsw algorithm (effective with -a bwtsw) [10000000] -6 index files named as .64. instead of .

Warning: -a bwtsw' does not work for short genomes, while-a is' and `-a div' do not work not for long genomes.

(ChIA-PET) sun@sun-ubuntu:~$ bwa index /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta [bwa_index] Pack FASTA... 4.00 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=774848718, availableWord=66520980 [BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 194075422 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 277685918 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 351995134 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 418037342 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 476731822 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 528895614 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 575254878 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 616455102 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 653069966 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 685609294 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 714526318 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 740223806 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 763059758 characters processed. [bwt_gen] Finished constructing BWT in 146 iterations. [bwa_index] 382.05 seconds elapse. [bwa_index] Update BWT... 3.25 sec [bwa_index] Pack forward-only FASTA... 2.41 sec [bwa_index] Construct SA from BWT and Occ... 144.31 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta [main] Real time: 582.788 sec; CPU: 536.028 sec (ChIA-PET) sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output ChIA-PET_MH63 --prefix ChIA-PET --thread 20 [Sun Sep 08 22:04:52 CST 2019] start ChIA-PET analysis [Sun Sep 08 22:04:52 CST 2019] Step1: Linker filtering ... Error: parameter error. The maximun numbers of threads must <= 16 (ChIA-PET) sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output ChIA-PET_MH63 --prefix ChIA-PET --thread 16 [Sun Sep 08 22:05:21 CST 2019] start ChIA-PET analysis [Sun Sep 08 22:05:21 CST 2019] Step1: Linker filtering ... [Sun Sep 08 22:18:49 CST 2019] Step2: Mapping to genome ... [Sun Sep 08 22:19:16 CST 2019] Step3: Removing redundancy ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.dist.txt doesn't exist [Sun Sep 08 22:19:16 CST 2019] Step4: Categorization of PETs ... [Sun Sep 08 22:19:16 CST 2019] start PetClassification ... [Sun Sep 08 22:19:16 CST 2019] start loading PETs from ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Sun Sep 08 22:19:16 CST 2019] 0.0M PETs read from ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Sun Sep 08 22:19:16 CST 2019] Step5: Interaction Calling ... [Sun Sep 08 22:19:16 CST 2019] start PetCluster2 ... number of clusters = 0 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln1 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln2 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor2 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1.tagCount.txt doesn't exist 错误于file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: 警告信息： In file(file, "rt") : 无法打开文件'ChIA-PET_MH63/ChIA-PET/ChIA-PET.petCount.tagCount.txt': 没有那个文件或目录停止执行 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:16 CST 2019] Step6: Peak Calling ... [Sun Sep 08 22:19:16 CST 2019] start BindingSites ... this.peakMode = 2 [Sun Sep 08 22:19:16 CST 2019] start loading PETs from ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet [Sun Sep 08 22:19:16 CST 2019] totally 0M PETs read from ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet IN peakMode 2 Number of peaks: 0 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K.temp doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K.temp doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.10K_10K doesn't exist [1] "/usr/lib/R/bin/exec/R"
[2] "--vanilla"
[3] "--slave"
[4] "--args"
[5] "genomeLengthStr=4E8"
[6] "genomeCoverageRatioStr=0.8"
[7] "extensionLengthStr=500"
[8] "outPrefix=ChIA-PET_MH63/ChIA-PET/ChIA-PET" assigned /usr/lib/R/bin/exec/R the value of TRUE assigned --vanilla the value of TRUE assigned --slave the value of TRUE assigned --args the value of TRUE assigned genomeLengthStr the value of | 4E8 | assigned genomeCoverageRatioStr the value of | 0.8 | assigned extensionLengthStr the value of | 500 | assigned outPrefix the value of | ChIA-PET_MH63/ChIA-PET/ChIA-PET | 错误于file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: 警告信息： In file(file, "rt") : 无法打开文件'ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.txt': 没有那个文件或目录停止执行 [Sun Sep 08 22:19:17 CST 2019] start TagCountForPeaks ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.pvalue.pois.txt doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.compact doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.long doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:18 CST 2019] Step7: Visualizing ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [1] "Package grid is loaded correctly" [1] "Trying to install package xtable" Loading required package: grid Loading required package: xtable Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) install.packages(pkg, repos = "http://cran.us.r-project.org", 里有警告: 'lib = "/usr/local/lib/R/site-library"' is not writable 错误于install.packages(pkg, repos = "http://cran.us.r-project.org", : unable to install packages Calls: check_pkg -> install.packages 停止执行 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:18 CST 2019] finish ChIA-PET analysis

for output option, please specify the absolute path of the output directory.--output: specifies the directory to store the output data from ChIA-PET Tool V3, note: please specify the absolute path of output directory.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/

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From："Mustela-sibirica" notifications@github.com To："GuoliangLi-HZAU/ChIA-PET_Tool_V3" ChIA-PET_Tool_V3@noreply.github.com Subject：[GuoliangLi-HZAU/ChIA-PET_Tool_V3] Error in running. (#1) Date：2019-09-08 22:26:49I have something wrong in running, but I don't konw why. The information below: java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output ChIA-PET_MH63 --prefix ChIA-PET --thread 16 [Sun Sep 08 22:05:21 CST 2019] start ChIA-PET analysis [Sun Sep 08 22:05:21 CST 2019] Step1: Linker filtering ... [Sun Sep 08 22:18:49 CST 2019] Step2: Mapping to genome ... [Sun Sep 08 22:19:16 CST 2019] Step3: Removing redundancy ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.dist.txt doesn't exist [Sun Sep 08 22:19:16 CST 2019] Step4: Categorization of PETs ... [Sun Sep 08 22:19:16 CST 2019] start PetClassification ... [Sun Sep 08 22:19:16 CST 2019] start loading PETs from ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Sun Sep 08 22:19:16 CST 2019] 0.0M PETs read from ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Sun Sep 08 22:19:16 CST 2019] Step5: Interaction Calling ... [Sun Sep 08 22:19:16 CST 2019] start PetCluster2 ... number of clusters = 0 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln1 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln2 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor2 doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1.tagCount.txt doesn't exist 错误于file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: 警告信息： In file(file, "rt") : 无法打开文件'ChIA-PET_MH63/ChIA-PET/ChIA-PET.petCount.tagCount.txt': 没有那个文件或目录停止执行 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:16 CST 2019] Step6: Peak Calling ... [Sun Sep 08 22:19:16 CST 2019] start BindingSites ... this.peakMode = 2 [Sun Sep 08 22:19:16 CST 2019] start loading PETs from ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet [Sun Sep 08 22:19:16 CST 2019] totally 0M PETs read from ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet IN peakMode 2 Number of peaks: 0 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K.temp doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K.temp doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.10K_10K doesn't exist [1] "/usr/lib/R/bin/exec/R" [2] "--vanilla" [3] "--slave" [4] "--args" [5] "genomeLengthStr=4E8" [6] "genomeCoverageRatioStr=0.8" [7] "extensionLengthStr=500" [8] "outPrefix=ChIA-PET_MH63/ChIA-PET/ChIA-PET" assigned /usr/lib/R/bin/exec/R the value of TRUE assigned --vanilla the value of TRUE assigned --slave the value of TRUE assigned --args the value of TRUE assigned genomeLengthStr the value of | 4E8 | assigned genomeCoverageRatioStr the value of | 0.8 | assigned extensionLengthStr the value of | 500 | assigned outPrefix the value of | ChIA-PET_MH63/ChIA-PET/ChIA-PET | 错误于file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: 警告信息： In file(file, "rt") : 无法打开文件'ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.txt': 没有那个文件或目录停止执行 [Sun Sep 08 22:19:17 CST 2019] start TagCountForPeaks ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.pvalue.pois.txt doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.compact doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.long doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:18 CST 2019] Step7: Visualizing ... Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [1] "Package grid is loaded correctly" [1] "Trying to install package xtable" Loading required package: grid Loading required package: xtable Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) install.packages(pkg, repos = "http://cran.us.r-project.org", 里有警告: 'lib = "/usr/local/lib/R/site-library"' is not writable 错误于install.packages(pkg, repos = "http://cran.us.r-project.org", : unable to install packages Calls: check_pkg -> install.packages 停止执行 Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist Error: ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.FDRfiltered.txt doesn't exist [Sun Sep 08 22:19:18 CST 2019] finish ChIA-PET analysis

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Thanks for Answering! I corrected the path,but still get the error. And the run time is too short and file is too small, the bwa align seem to not work? sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output /media/sun/WD-1000G/ChIA-PET_MH63 --prefix ChIA-PET --thread 16 [Mon Sep 09 23:13:37 CST 2019] start ChIA-PET analysis [Mon Sep 09 23:13:37 CST 2019] Step1: Linker filtering ... [Mon Sep 09 23:52:03 CST 2019] Step2: Mapping to genome ... [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [Mon Sep 09 23:52:32 CST 2019] Step3: Removing redundancy ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.dist.txt doesn't exist [Mon Sep 09 23:52:32 CST 2019] Step4: Categorization of PETs ... [Mon Sep 09 23:52:32 CST 2019] start PetClassification ... [Mon Sep 09 23:52:32 CST 2019] start loading PETs from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Mon Sep 09 23:52:32 CST 2019] 0.0M PETs read from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Mon Sep 09 23:52:32 CST 2019] Step5: Interaction Calling ... [Mon Sep 09 23:52:32 CST 2019] start PetCluster2 ... number of clusters = 0 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln1 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln2 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor2 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1.tagCount.txt doesn't exist Error in file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: Warning message: In file(file, "rt") : 无法打开文件'/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.petCount.tagCount.txt': 没有那个文件或目录停止执行 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:33 CST 2019] Step6: Peak Calling ... [Mon Sep 09 23:52:33 CST 2019] start BindingSites ... this.peakMode = 2 [Mon Sep 09 23:52:33 CST 2019] start loading PETs from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet [Mon Sep 09 23:52:33 CST 2019] totally 0M PETs read from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet IN peakMode 2 Number of peaks: 0 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K.temp doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K.temp doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.10K_10K doesn't exist [1] "/usr/lib/R/bin/exec/R" [2] "--vanilla" [3] "--slave" [4] "--args" [5] "genomeLengthStr=4E8" [6] "genomeCoverageRatioStr=0.8" [7] "extensionLengthStr=500" [8] "outPrefix=/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET" assigned /usr/lib/R/bin/exec/R the value of TRUE assigned --vanilla the value of TRUE assigned --slave the value of TRUE assigned --args the value of TRUE assigned genomeLengthStr the value of | 4E8 | assigned genomeCoverageRatioStr the value of | 0.8 | assigned extensionLengthStr the value of | 500 | assigned outPrefix the value of | /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET | Error in file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: Warning message: In file(file, "rt") : 无法打开文件'/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.txt': 没有那个文件或目录停止执行 [Mon Sep 09 23:52:33 CST 2019] start TagCountForPeaks ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.pvalue.pois.txt doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.compact doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.long doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:33 CST 2019] Step7: Visualizing ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [1] "Package grid is loaded correctly" [1] "Package xtable is loaded correctly" [1] "Package RCircos is loaded correctly" null device 1 null device 1 null device 1 Loading required package: grid Loading required package: xtable Loading required package: RCircos Error in FUN(X[[i]], ...) : no lines available in input Calls: draw_barplot -> lapply -> FUN 停止执行 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:34 CST 2019] finish ChIA-PET analysis

The early error message is: [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file.

Please check your mapping file.

Best regards, Guoliang

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："Mustela-sibirica" 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] Error in running. (#1) Date：2019-09-09 23:55:55> absolute Thanks for Answering! I corrected the path,but still get the error. sun@sun-ubuntu:~$ java -jar /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /media/sun/WD-1000G/ChIA-PET/SRR9054440_1.fastq.gz --fastq2 /media/sun/WD-1000G/ChIA-PET/SRR9054440_2.fastq.gz --linker /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 14 --GENOME_INDEX /media/sun/WD-1000G/ChIA-PET/MH63RS2.LNNK00000000.fasta --GENOME_LENGTH 4E8 --CHROM_SIZE_INFO /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63.chromSize.txt --CYTOBAND_DATA /home/sun/anaconda3/envs/ChIA-PET/ChIA-PET_Tool_V3/chromInfo/mh63_cytoBandIdeo.txt --SPECIES 3 --output /media/sun/WD-1000G/ChIA-PET_MH63 --prefix ChIA-PET --thread 16 [Mon Sep 09 23:13:37 CST 2019] start ChIA-PET analysis [Mon Sep 09 23:13:37 CST 2019] Step1: Linker filtering ... [Mon Sep 09 23:52:03 CST 2019] Step2: Mapping to genome ... [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [samopen] SAM header is present: 12 sequences. [sam_read1] reference 'SN:Chr12 LN:26156356 ' is recognized as '*'. [main_samview] truncated file. [Mon Sep 09 23:52:32 CST 2019] Step3: Removing redundancy ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.dist.txt doesn't exist [Mon Sep 09 23:52:32 CST 2019] Step4: Categorization of PETs ... [Mon Sep 09 23:52:32 CST 2019] start PetClassification ... [Mon Sep 09 23:52:32 CST 2019] start loading PETs from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Mon Sep 09 23:52:32 CST 2019] 0.0M PETs read from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.bedpe.selected.pet.txt [Mon Sep 09 23:52:32 CST 2019] Step5: Interaction Calling ... [Mon Sep 09 23:52:32 CST 2019] start PetCluster2 ... number of clusters = 0 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln1 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.aln2 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor2 doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered.anchor1.tagCount.txt doesn't exist Error in file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: Warning message: In file(file, "rt") : 无法打开文件'/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.petCount.tagCount.txt': 没有那个文件或目录停止执行 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.filtered doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:33 CST 2019] Step6: Peak Calling ... [Mon Sep 09 23:52:33 CST 2019] start BindingSites ... this.peakMode = 2 [Mon Sep 09 23:52:33 CST 2019] start loading PETs from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet [Mon Sep 09 23:52:33 CST 2019] totally 0M PETs read from /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.spet IN peakMode 2 Number of peaks: 0 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K.temp doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K.temp doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.10K_10K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.10K_10K doesn't exist [1] "/usr/lib/R/bin/exec/R" [2] "--vanilla" [3] "--slave" [4] "--args" [5] "genomeLengthStr=4E8" [6] "genomeCoverageRatioStr=0.8" [7] "extensionLengthStr=500" [8] "outPrefix=/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET" assigned /usr/lib/R/bin/exec/R the value of TRUE assigned --vanilla the value of TRUE assigned --slave the value of TRUE assigned --args the value of TRUE assigned genomeLengthStr the value of | 4E8 | assigned genomeCoverageRatioStr the value of | 0.8 | assigned extensionLengthStr the value of | 500 | assigned outPrefix the value of | /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET | Error in file(file, "rt") : 无法打开链结 Calls: as.matrix -> read.table -> file 此外: Warning message: In file(file, "rt") : 无法打开文件'/media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.spetCounts.txt': 没有那个文件或目录停止执行 [Mon Sep 09 23:52:33 CST 2019] start TagCountForPeaks ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.pvalue.pois.txt doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.compact doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.long doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.5K_5K doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:33 CST 2019] Step7: Visualizing ... Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist [1] "Package grid is loaded correctly" [1] "Package xtable is loaded correctly" [1] "Package RCircos is loaded correctly" null device 1 null device 1 null device 1 Loading required package: grid Loading required package: xtable Loading required package: RCircos Error in FUN(X[[i]], ...) : no lines available in input Calls: draw_barplot -> lapply -> FUN 停止执行 Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.cluster.FDRfiltered.txt doesn't exist Error: /media/sun/WD-1000G/ChIA-PET_MH63/ChIA-PET/ChIA-PET.peak.FDRfiltered.txt doesn't exist [Mon Sep 09 23:52:34 CST 2019] finish ChIA-PET analysis

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I also have the same errors

GuoliangLi-HZAU / ChIA-PET_Tool_V3

Error in running. #1